Variant report

Variant	rs6560593
Chromosome Location	chr9:71752270-71752271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71736348..71739276-chr9:71751743..71753516,2	MCF-7	breast:
2	chr9:71751405..71753557-chr9:71754610..71757893,3	MCF-7	breast:
3	chr9:71745166..71747792-chr9:71751582..71754371,2	K562	blood:
4	chr9:71735718..71737415-chr9:71751707..71753369,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119139	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10156634	0.84[AMR][1000 genomes]
rs10156651	0.84[AMR][1000 genomes]
rs10735653	0.84[AMR][1000 genomes]
rs12551317	0.81[AMR][1000 genomes]
rs2993817	0.81[AMR][1000 genomes]
rs2993822	0.81[AMR][1000 genomes]
rs4567104	0.92[AMR][1000 genomes]
rs4745625	0.84[AMR][1000 genomes]
rs4745626	0.84[AMR][1000 genomes]
rs4745627	0.88[AMR][1000 genomes]
rs6560586	0.81[AMR][1000 genomes]
rs7030890	0.85[AMR][1000 genomes]
rs7875573	0.96[AMR][1000 genomes]
rs9411202	0.81[AMR][1000 genomes]
rs9411203	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv1051798	chr9:71511805-71792032	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv466397	chr9:71574757-71843023	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv614550	chr9:71574757-71843023	Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	nsv1050692	chr9:71578494-71843023	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv893416	chr9:71597840-71888601	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
18	nsv1040539	chr9:71600042-71844108	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	nsv540149	chr9:71600042-71844108	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
20	nsv949664	chr9:71607398-71842391	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
21	nsv948708	chr9:71632265-71842391	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
22	nsv1037787	chr9:71635338-71807648	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
23	nsv540151	chr9:71635338-71807648	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
24	nsv817209	chr9:71675454-71829412	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
25	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
26	nsv508550	chr9:71679166-71809433	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
27	nsv6550	chr9:71714144-71760048	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
28	esv1798602	chr9:71718195-71764191	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71738000-71778200	Weak transcription	Primary T cells from cord blood	blood
2	chr9:71738200-71752400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:71738200-71757000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:71738200-71770600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:71743600-71752800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:71745400-71770600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:71746000-71752800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:71746000-71754800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:71746200-71764400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:71746400-71758200	Weak transcription	Brain Anterior Caudate	brain
11	chr9:71746400-71758200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr9:71746400-71759200	Weak transcription	Brain Angular Gyrus	brain
13	chr9:71746400-71783200	Weak transcription	Small Intestine	intestine
14	chr9:71747000-71768600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:71747000-71775600	Weak transcription	Hela-S3	cervix
16	chr9:71747200-71757000	Weak transcription	Fetal Lung	lung
17	chr9:71747200-71758200	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:71747200-71764200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:71747200-71764200	Weak transcription	Fetal Kidney	kidney
20	chr9:71747200-71766800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr9:71747200-71769800	Weak transcription	Placenta	Placenta
22	chr9:71747400-71757000	Weak transcription	Colonic Mucosa	Colon
23	chr9:71747400-71758200	Weak transcription	Brain Substantia Nigra	brain
24	chr9:71747600-71764200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:71747600-71764400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr9:71747800-71757000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:71747800-71758400	Weak transcription	HMEC	breast
28	chr9:71747800-71764200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:71748400-71764200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr9:71748400-71764800	Weak transcription	Aorta	Aorta
31	chr9:71749000-71754400	Weak transcription	Right Ventricle	heart
32	chr9:71749200-71757000	Weak transcription	Psoas Muscle	Psoas
33	chr9:71749600-71752600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr9:71749600-71755200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr9:71749600-71764200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr9:71749800-71754400	Weak transcription	Gastric	stomach
37	chr9:71749800-71754800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr9:71749800-71759600	Weak transcription	Pancreas	Pancrea
39	chr9:71749800-71761800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:71749800-71764200	Weak transcription	Fetal Stomach	stomach
41	chr9:71749800-71770200	Weak transcription	Esophagus	oesophagus
42	chr9:71749800-71770200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr9:71749800-71780600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr9:71750000-71757000	Weak transcription	NHEK	skin
45	chr9:71750000-71764200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr9:71750000-71764200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr9:71750200-71752600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr9:71750400-71752600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr9:71751200-71754200	Weak transcription	Fetal Heart	heart
50	chr9:71751200-71754200	Strong transcription	HepG2	liver

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