Variant report

Variant	rs4960046
Chromosome Location	chr6:4901921-4901922
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4900734..4903039-chr6:4905206..4906840,2	MCF-7	breast:
2	chr6:4898972..4902632-chr6:4903535..4907874,4	MCF-7	breast:
3	chr6:4901839..4904392-chr6:4905439..4907191,2	K562	blood:
4	chr6:4897821..4901952-chr6:4908622..4912007,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11967994	0.85[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs11968021	0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap]
rs1265332	0.86[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap]
rs1265333	0.86[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap]
rs1265335	0.85[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs13199417	1.00[CHB][hapmap]
rs13212871	1.00[CHB][hapmap]
rs17138856	0.86[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap]
rs17138859	0.91[CHB][hapmap]
rs17138959	1.00[CHB][hapmap]
rs17138966	1.00[CHB][hapmap]
rs184588	0.85[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs1891045	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2326553	1.00[CHB][hapmap]
rs233476	0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap]
rs3748078	0.86[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap]
rs62384662	0.88[EUR][1000 genomes]
rs62384663	0.88[EUR][1000 genomes]
rs62384665	0.85[EUR][1000 genomes]
rs6924037	0.87[EUR][1000 genomes]
rs808593	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs808598	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs808600	0.86[EUR][1000 genomes]
rs808606	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs808607	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs808635	0.87[EUR][1000 genomes]
rs811251	1.00[CHB][hapmap]
rs9378917	0.87[EUR][1000 genomes]
rs9378919	0.87[EUR][1000 genomes]
rs9392640	0.87[EUR][1000 genomes]
rs9405786	0.84[EUR][1000 genomes]
rs9502250	0.89[CHB][hapmap]
rs9504254	0.86[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap]
rs9504284	0.92[CHB][hapmap]

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	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv970734	chr6:4898790-4906391	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4878200-4905200	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:4879600-4906200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:4880400-4907800	Weak transcription	Small Intestine	intestine
4	chr6:4882800-4909000	Weak transcription	Brain Anterior Caudate	brain
5	chr6:4884800-4903800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:4885000-4908200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:4888000-4906400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:4889200-4906400	Weak transcription	NHLF	lung
9	chr6:4890600-4913800	Weak transcription	Hela-S3	cervix
10	chr6:4891200-4905600	Weak transcription	Fetal Kidney	kidney
11	chr6:4891200-4907400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:4891400-4906400	Weak transcription	Fetal Heart	heart
13	chr6:4892800-4906400	Weak transcription	HUVEC	blood vessel
14	chr6:4892800-4906600	Weak transcription	Osteobl	bone
15	chr6:4893200-4912600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:4893400-4903400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:4893400-4903400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:4893400-4906600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:4893400-4906600	Weak transcription	Thymus	Thymus
20	chr6:4893400-4909000	Weak transcription	Brain Angular Gyrus	brain
21	chr6:4893600-4905000	Weak transcription	Colonic Mucosa	Colon
22	chr6:4893600-4910200	Weak transcription	Esophagus	oesophagus
23	chr6:4893600-4914000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:4894600-4904000	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:4894600-4905600	Weak transcription	Right Ventricle	heart
26	chr6:4894800-4906600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:4895000-4917000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:4895200-4909000	Weak transcription	Adipose Nuclei	Adipose
29	chr6:4896000-4906600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:4896400-4903400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:4896800-4902000	Weak transcription	Gastric	stomach
32	chr6:4896800-4903800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:4896800-4906600	Weak transcription	Spleen	Spleen
34	chr6:4896800-4907200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:4897000-4906400	Weak transcription	Fetal Thymus	thymus
36	chr6:4897000-4906600	Weak transcription	Aorta	Aorta
37	chr6:4897800-4906200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr6:4898000-4907000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:4898800-4910200	Weak transcription	Psoas Muscle	Psoas
40	chr6:4899000-4902000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:4899000-4902000	Weak transcription	Lung	lung
42	chr6:4899000-4902800	Weak transcription	Fetal Lung	lung
43	chr6:4899000-4903000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:4899000-4903400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr6:4899000-4903400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:4899000-4903800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:4899000-4905000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:4899000-4909000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:4899200-4902000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:4899200-4902000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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