Variant report

Variant	rs820094
Chromosome Location	chr6:35021626-35021627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:35021580-35021730	NHLF	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:35020474..35024244-chr6:35026178..35030264,6	K562	blood:
2	chr6:35020203..35022159-chr6:35023011..35024992,4	K562	blood:
3	chr6:35016131..35018255-chr6:35020438..35022614,2	MCF-7	breast:

Variant related genes	Relation type
ANKS1A	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1093985	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13191889	0.87[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs1568705	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16896390	0.81[JPT][hapmap]
rs16896553	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs2049316	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2140420	0.81[CEU][hapmap]
rs2689097	0.80[EUR][1000 genomes]
rs2762342	0.82[EUR][1000 genomes]
rs2762350	0.81[CEU][hapmap]
rs2820224	0.91[ASN][1000 genomes]
rs2820229	0.81[CEU][hapmap]
rs2820230	0.96[ASN][1000 genomes]
rs3800424	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs3800426	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3800430	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs3800433	0.91[JPT][hapmap]
rs3823437	0.84[ASN][1000 genomes]
rs6937805	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707967	0.84[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72537461	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs820068	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs820073	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs820074	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs820075	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs820076	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs820078	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs820079	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs820080	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs820081	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs820084	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs820086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs820087	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs820088	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs820089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs820091	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs820092	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs820093	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs820096	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs820097	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs820098	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs865353	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357193	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9469933	0.91[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34994600-35036000	Weak transcription	K562	blood
2	chr6:35014600-35022200	Weak transcription	NHEK	skin
3	chr6:35015200-35021800	Enhancers	Left Ventricle	heart
4	chr6:35015600-35021800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:35015800-35044200	Weak transcription	HMEC	breast
6	chr6:35016200-35022400	Weak transcription	Pancreas	Pancrea
7	chr6:35016200-35055000	Weak transcription	Hela-S3	cervix
8	chr6:35016400-35023800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:35016800-35026400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr6:35016800-35026800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr6:35016800-35027800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:35016800-35028000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:35016800-35028000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr6:35017000-35026000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr6:35017000-35026200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr6:35017000-35026200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:35017200-35021800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:35017200-35022000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:35017400-35021800	Enhancers	Brain Substantia Nigra	brain
20	chr6:35017400-35022600	Weak transcription	Gastric	stomach
21	chr6:35017400-35028000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:35017400-35028600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:35017600-35021800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:35017600-35028000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr6:35017600-35036200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr6:35017800-35021800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:35017800-35024800	Weak transcription	Fetal Heart	heart
28	chr6:35017800-35027600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:35017800-35053000	Weak transcription	Small Intestine	intestine
30	chr6:35018000-35021800	Weak transcription	Thymus	Thymus
31	chr6:35018200-35022800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:35018200-35025400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:35018200-35025600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr6:35018400-35021800	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr6:35018400-35021800	Weak transcription	Osteobl	bone
36	chr6:35018400-35052800	Weak transcription	Fetal Kidney	kidney
37	chr6:35018600-35022000	Enhancers	Brain Cingulate Gyrus	brain
38	chr6:35018600-35025000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:35018600-35027800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr6:35018600-35051000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr6:35018800-35021800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:35018800-35022200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:35018800-35022600	Genic enhancers	HSMMtube	muscle
44	chr6:35018800-35026600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:35018800-35029000	Weak transcription	NHDF-Ad	bronchial
46	chr6:35018800-35038200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr6:35018800-35060600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr6:35019000-35022600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:35019000-35022600	Weak transcription	Aorta	Aorta
50	chr6:35019400-35022000	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links