Variant report

Variant	rs3800426
Chromosome Location	chr6:35009196-35009197
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35007638..35010426-chr6:35012141..35014563,2	K562	blood:
2	chr6:35008594..35011463-chr6:35016010..35018720,2	MCF-7	breast:
3	chr6:34968308..34970921-chr6:35006790..35009720,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1093985	0.93[ASN][1000 genomes]
rs13191889	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1568705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16896390	0.80[JPT][hapmap]
rs16896553	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2049316	0.85[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2820223	0.91[GIH][hapmap]
rs2820224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2820230	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800424	0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs3800430	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs3800433	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs3823437	0.86[ASN][1000 genomes]
rs3823438	0.85[CEU][hapmap]
rs6937805	0.90[ASN][1000 genomes]
rs707967	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs72537461	0.93[ASN][1000 genomes]
rs820068	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs820073	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs820074	0.91[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs820075	0.87[ASN][1000 genomes]
rs820076	0.95[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs820078	0.85[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs820079	0.84[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs820080	0.94[ASN][1000 genomes]
rs820081	0.94[ASN][1000 genomes]
rs820084	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs820086	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs820087	0.94[ASN][1000 genomes]
rs820088	0.93[ASN][1000 genomes]
rs820089	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs820091	0.92[ASN][1000 genomes]
rs820092	0.95[ASN][1000 genomes]
rs820094	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs820096	0.96[ASN][1000 genomes]
rs820097	0.86[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs820098	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs865353	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9357193	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs9469933	0.83[CHD][hapmap];0.90[JPT][hapmap];0.85[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3800426	ANKS1A	cis	parietal	SCAN
rs3800426	TAF11	cis	cerebellum	SCAN
rs3800426	ANKS1A	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34939400-35016000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:34986200-35015000	Weak transcription	Primary B cells from peripheral blood	blood
3	chr6:34986400-35011800	Weak transcription	Dnd41	blood
4	chr6:34986800-35014800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:34987000-35015800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:34987400-35015800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:34992800-35011800	Weak transcription	Brain Germinal Matrix	brain
8	chr6:34993800-35014600	Weak transcription	Fetal Brain Male	brain
9	chr6:34994200-35014400	Weak transcription	NHLF	lung
10	chr6:34994600-35036000	Weak transcription	K562	blood
11	chr6:34995000-35013800	Weak transcription	Hela-S3	cervix
12	chr6:34996000-35015200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr6:34996200-35010000	Weak transcription	Ovary	ovary
14	chr6:34999800-35014600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr6:35003200-35012000	Weak transcription	Thymus	Thymus
16	chr6:35003600-35010400	Weak transcription	Pancreas	Pancrea
17	chr6:35003800-35010400	Weak transcription	Gastric	stomach
18	chr6:35003800-35012000	Strong transcription	Fetal Intestine Small	intestine
19	chr6:35003800-35014600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:35004000-35009400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:35004000-35010400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:35004000-35010400	Weak transcription	Esophagus	oesophagus
23	chr6:35004000-35012200	Weak transcription	Fetal Thymus	thymus
24	chr6:35004200-35010200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:35004200-35010200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:35004200-35010400	Weak transcription	Colonic Mucosa	Colon
27	chr6:35004200-35011800	Weak transcription	Fetal Kidney	kidney
28	chr6:35004200-35011800	Weak transcription	HMEC	breast
29	chr6:35004200-35012800	Weak transcription	Small Intestine	intestine
30	chr6:35004400-35009400	Weak transcription	HUVEC	blood vessel
31	chr6:35004400-35010600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:35004400-35011000	Weak transcription	Stomach Mucosa	stomach
33	chr6:35004800-35012200	Weak transcription	Fetal Lung	lung
34	chr6:35005400-35012000	Strong transcription	Fetal Intestine Large	intestine
35	chr6:35005600-35010800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr6:35005800-35011000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:35006000-35009800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:35006000-35012000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr6:35006000-35014200	Genic enhancers	HSMMtube	muscle
40	chr6:35006200-35009400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:35006200-35009600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr6:35006200-35009600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr6:35006200-35010000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:35006200-35010200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:35006200-35010200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:35006200-35010200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:35006200-35010200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:35006200-35010400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:35006200-35010600	Weak transcription	Fetal Heart	heart
50	chr6:35006200-35010800	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links