Variant report

Variant	rs3800424
Chromosome Location	chr6:35011446-35011447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35002561..35006786-chr6:35010332..35014287,4	K562	blood:
2	chr6:35010474..35014059-chr6:35017313..35020799,3	K562	blood:
3	chr6:35008594..35011463-chr6:35016010..35018720,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1093985	0.80[ASN][1000 genomes]
rs12212217	0.87[JPT][hapmap]
rs1568705	0.91[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs16896390	0.91[JPT][hapmap]
rs16896553	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1996913	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs2049316	0.89[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2140418	0.87[JPT][hapmap]
rs2820224	0.81[ASN][1000 genomes]
rs2820230	0.86[ASN][1000 genomes]
rs3800426	0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs3800430	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3800433	0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[ASN][1000 genomes]
rs3823437	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930756	0.84[ASN][1000 genomes]
rs707967	0.81[CHD][hapmap]
rs72537461	0.80[ASN][1000 genomes]
rs820068	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs820073	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs820074	0.83[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs820076	0.91[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs820080	0.81[ASN][1000 genomes]
rs820081	0.81[ASN][1000 genomes]
rs820084	0.91[CHD][hapmap]
rs820087	0.81[ASN][1000 genomes]
rs820088	0.80[ASN][1000 genomes]
rs820089	0.93[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs820092	0.82[ASN][1000 genomes]
rs820094	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs820096	0.83[ASN][1000 genomes]
rs820098	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs865353	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs9357193	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9394265	0.80[CEU][hapmap]
rs9394267	0.80[CEU][hapmap]
rs9469933	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3800424	TAF11	cis	cerebellum	SCAN
rs3800424	UHRF1BP1	cis	parietal	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	chr6:34999800-35014600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr6:35003200-35012000	Weak transcription	Thymus	Thymus
15	chr6:35003800-35012000	Strong transcription	Fetal Intestine Small	intestine
16	chr6:35003800-35014600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:35004000-35012200	Weak transcription	Fetal Thymus	thymus
18	chr6:35004200-35011800	Weak transcription	Fetal Kidney	kidney
19	chr6:35004200-35011800	Weak transcription	HMEC	breast
20	chr6:35004200-35012800	Weak transcription	Small Intestine	intestine
21	chr6:35004800-35012200	Weak transcription	Fetal Lung	lung
22	chr6:35005400-35012000	Strong transcription	Fetal Intestine Large	intestine
23	chr6:35006000-35012000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:35006000-35014200	Genic enhancers	HSMMtube	muscle
25	chr6:35006200-35011800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:35006200-35012000	Weak transcription	NHDF-Ad	bronchial
27	chr6:35006200-35012200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:35006200-35014200	Weak transcription	Osteobl	bone
29	chr6:35006400-35011800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr6:35006400-35012000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:35006600-35011800	Weak transcription	HSMM	muscle
32	chr6:35007200-35012000	Enhancers	Rectal Smooth Muscle	rectum
33	chr6:35007400-35014200	Enhancers	Right Atrium	heart
34	chr6:35008600-35012000	Enhancers	Left Ventricle	heart
35	chr6:35008600-35014200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr6:35008800-35011800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:35008800-35011800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:35008800-35012600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:35009000-35012200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:35009000-35014600	Enhancers	Right Ventricle	heart
41	chr6:35009000-35015000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:35009000-35018800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:35009200-35016200	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr6:35009400-35011800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:35009400-35012000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr6:35009400-35012400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
47	chr6:35009400-35014600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr6:35009400-35016800	Enhancers	HUVEC	blood vessel
49	chr6:35009600-35011800	Weak transcription	Liver	Liver
50	chr6:35009600-35011800	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links