Variant report

Variant	rs9366616
Chromosome Location	chr6:25315153-25315154
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25314031..25316618-chr6:25318937..25320645,2	MCF-7	breast:
2	chr6:25314690..25316229-chr6:25317879..25319908,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs12055697	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16890366	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1883393	0.94[ASN][1000 genomes]
rs2143023	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2690042	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2690047	1.00[CEU][hapmap]
rs2690056	1.00[CEU][hapmap]
rs2744273	1.00[CEU][hapmap]
rs2744274	1.00[CEU][hapmap]
rs2744287	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4712904	0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4712905	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4712906	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712907	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55967593	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs55999195	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58191968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60084615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6456664	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456665	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456666	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456668	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6903148	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906812	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6913606	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913886	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914439	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6914514	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914654	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6914798	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914930	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915270	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6917631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6921343	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923529	0.96[ASN][1000 genomes]
rs6927238	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6936496	1.00[CEU][hapmap]
rs6938281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6939174	1.00[CEU][hapmap]
rs730711	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs73392399	0.96[ASN][1000 genomes]
rs73396126	0.90[ASN][1000 genomes]
rs7741580	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7743750	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7746942	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746969	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755701	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756143	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758529	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759796	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7759828	0.81[ASN][1000 genomes]
rs7759879	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7760067	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7760151	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7764111	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9295654	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348671	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9356974	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358852	1.00[CEU][hapmap]
rs9366617	0.82[AFR][1000 genomes]
rs9379752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9393639	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9461132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461134	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999039	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv16338	chr6:25312436-25315638	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25303400-25315400	Weak transcription	Fetal Kidney	kidney
2	chr6:25305000-25324400	Weak transcription	Left Ventricle	heart
3	chr6:25306600-25331400	Weak transcription	Spleen	Spleen
4	chr6:25310200-25316800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:25310400-25319400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr6:25311600-25315400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:25311600-25317200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:25311600-25317200	Enhancers	Fetal Lung	lung
9	chr6:25312000-25315600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:25312000-25315600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:25312000-25324200	Weak transcription	Esophagus	oesophagus
12	chr6:25312000-25324200	Weak transcription	Pancreas	Pancrea
13	chr6:25312200-25315600	Weak transcription	Right Atrium	heart
14	chr6:25312200-25316000	Weak transcription	Gastric	stomach
15	chr6:25312600-25315600	Weak transcription	Fetal Thymus	thymus
16	chr6:25313400-25315400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:25313400-25315400	Weak transcription	Fetal Heart	heart
18	chr6:25313400-25329800	Weak transcription	Primary T cells from cord blood	blood
19	chr6:25313600-25315200	Enhancers	HSMMtube	muscle
20	chr6:25313600-25315400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:25313600-25316200	Enhancers	Fetal Brain Male	brain
22	chr6:25313600-25320200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:25313800-25315200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:25313800-25315400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:25313800-25315400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:25313800-25315400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:25313800-25315400	Weak transcription	Fetal Intestine Large	intestine
28	chr6:25313800-25315600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:25313800-25315600	Weak transcription	Aorta	Aorta
30	chr6:25313800-25315600	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:25313800-25315600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:25313800-25315800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:25313800-25316000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:25313800-25318400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:25313800-25318400	Weak transcription	Lung	lung
36	chr6:25313800-25322800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr6:25313800-25325800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr6:25313800-25326800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:25313800-25331400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:25314000-25318800	Weak transcription	Small Intestine	intestine
41	chr6:25314000-25325000	Weak transcription	Placenta	Placenta
42	chr6:25314200-25315400	Weak transcription	Fetal Intestine Small	intestine
43	chr6:25314200-25316000	Weak transcription	Ovary	ovary
44	chr6:25314200-25318400	Weak transcription	NHDF-Ad	bronchial
45	chr6:25314200-25319200	Weak transcription	Thymus	Thymus
46	chr6:25314600-25316800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:25314600-25317400	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr6:25314600-25317400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:25314800-25315200	Enhancers	Brain Cingulate Gyrus	brain
50	chr6:25314800-25315400	Enhancers	HUES48 Cell Line	embryonic stem cell

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