Variant report

Variant	rs6477960
Chromosome Location	chr9:115569502-115569503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115568175..115570231-chr9:115604790..115606325,2	K562	blood:
2	chr9:115568430..115571071-chr9:115577497..115580948,3	MCF-7	breast:
3	chr9:115568138..115570765-chr9:115571944..115575616,3	MCF-7	breast:
4	chr9:115565460..115568341-chr9:115568700..115570833,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10117017	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10117709	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10122712	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10732374	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10733595	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10739371	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10759587	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10759588	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10817391	0.88[ASN][1000 genomes]
rs10817392	0.86[ASN][1000 genomes]
rs10817395	0.88[ASN][1000 genomes]
rs10817396	0.87[ASN][1000 genomes]
rs10981513	0.88[ASN][1000 genomes]
rs10981515	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981516	0.88[ASN][1000 genomes]
rs10981519	0.88[ASN][1000 genomes]
rs10981521	0.88[ASN][1000 genomes]
rs10981522	0.88[ASN][1000 genomes]
rs10981523	0.88[ASN][1000 genomes]
rs11791125	0.88[ASN][1000 genomes]
rs11793016	0.88[ASN][1000 genomes]
rs1418408	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1539345	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2000204	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2096185	0.84[AFR][1000 genomes]
rs2096186	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2096187	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2153839	0.92[ASN][1000 genomes]
rs2185767	0.88[ASN][1000 genomes]
rs2645988	0.91[EUR][1000 genomes]
rs2796024	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4276760	0.88[ASN][1000 genomes]
rs4978504	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4979156	0.89[AFR][1000 genomes]
rs4979158	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4979162	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4979163	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4979164	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4979166	0.83[ASN][1000 genomes]
rs57546880	0.88[ASN][1000 genomes]
rs57672123	0.88[ASN][1000 genomes]
rs59645636	0.88[ASN][1000 genomes]
rs60989307	0.88[ASN][1000 genomes]
rs61626147	0.84[ASN][1000 genomes]
rs6477961	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7030460	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7032401	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7856199	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7868830	0.90[AFR][1000 genomes]
rs7871799	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7872308	0.90[AFR][1000 genomes]
rs787282	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs787283	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs787288	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7873644	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs870078	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs883462	0.88[ASN][1000 genomes]
rs9299210	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs999018	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv515899	chr9:115359049-115593870	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv34346	chr9:115360505-115581453	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1038999	chr9:115367078-115590950	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv2757350	chr9:115371397-115594108	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv2761275	chr9:115376461-115590962	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1035169	chr9:115378282-115573581	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1049451	chr9:115378282-115585109	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1047374	chr9:115378282-115590950	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1038306	chr9:115379305-115595695	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv540194	chr9:115379305-115595695	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1051909	chr9:115379505-115588377	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv540195	chr9:115379505-115588377	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv915763	chr9:115379600-115588349	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	esv3693040	chr9:115381164-115578065	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv515121	chr9:115383227-115585827	Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv1044168	chr9:115383253-115585109	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
19	nsv1048327	chr9:115383253-115589646	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
20	nsv1044381	chr9:115383253-115590950	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
21	nsv442163	chr9:115383255-115590578	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	esv35051	chr9:115383332-115573581	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
23	esv34763	chr9:115383332-115581453	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
24	nsv430090	chr9:115383445-115594445	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
25	nsv1041424	chr9:115389428-115590950	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
26	nsv1047625	chr9:115390759-115587347	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
27	nsv540196	chr9:115390759-115587347	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
28	nsv615198	chr9:115397206-115589251	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
29	nsv893733	chr9:115397206-115712068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
30	nsv1051808	chr9:115397891-115590950	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
31	esv34739	chr9:115409445-115581453	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
32	esv2422302	chr9:115550339-115656433	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115539000-115572800	Weak transcription	Spleen	Spleen
2	chr9:115545400-115570200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:115547200-115569600	Weak transcription	Left Ventricle	heart
4	chr9:115547200-115570000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr9:115547400-115570000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr9:115549800-115593600	Weak transcription	Thymus	Thymus
7	chr9:115552000-115580200	Weak transcription	Fetal Stomach	stomach
8	chr9:115552800-115572600	Weak transcription	Adipose Nuclei	Adipose
9	chr9:115552800-115572800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:115552800-115572800	Weak transcription	NHEK	skin
11	chr9:115552800-115593800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:115553000-115582000	Weak transcription	Esophagus	oesophagus
13	chr9:115553600-115579400	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:115555800-115572000	Weak transcription	Fetal Muscle Leg	muscle
15	chr9:115555800-115572400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:115555800-115572400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr9:115555800-115573000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr9:115555800-115581800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr9:115555800-115582000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:115555800-115582000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr9:115555800-115597400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:115556200-115580600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr9:115558200-115579200	Weak transcription	Osteobl	bone
24	chr9:115558400-115572800	Weak transcription	Right Ventricle	heart
25	chr9:115558800-115571800	Weak transcription	K562	blood
26	chr9:115558800-115572000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:115558800-115572600	Weak transcription	Lung	lung
28	chr9:115558800-115581800	Weak transcription	Aorta	Aorta
29	chr9:115559000-115580000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:115559200-115569800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:115559200-115571600	Weak transcription	Fetal Intestine Small	intestine
32	chr9:115559200-115572000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:115559400-115570000	Weak transcription	Ovary	ovary
34	chr9:115559400-115571800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr9:115559400-115572800	Weak transcription	Gastric	stomach
36	chr9:115559400-115581800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr9:115559400-115598400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr9:115559600-115593800	Weak transcription	Brain Germinal Matrix	brain
39	chr9:115562400-115572000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr9:115563200-115580600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr9:115564600-115593600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr9:115565000-115572600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr9:115565000-115600800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr9:115565200-115572200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:115565600-115569600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr9:115565600-115572600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr9:115565600-115572800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr9:115565600-115579400	Weak transcription	Liver	Liver
49	chr9:115565600-115600800	Weak transcription	HMEC	breast
50	chr9:115565800-115580400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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