Variant report

Variant	rs7640033
Chromosome Location	chr3:119017382-119017383
allele	A/T
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	WRNIP1	chr3:119017354-119017407	GM12878	blood:	n/a	n/a
2	RUNX3	chr3:119017003-119017431	GM12878	blood:	n/a	chr3:119017226-119017241
3	EBF1	chr3:119016832-119017410	GM12878	blood:	n/a	chr3:119017064-119017075 chr3:119017066-119017075 chr3:119017064-119017077 chr3:119017065-119017075
4	POLR2A	chr3:119017042-119017602	GM12878	blood:	n/a	n/a
5	RUNX3	chr3:119016973-119017419	GM12878	blood:	n/a	chr3:119017226-119017241

No.	Distal block	Cell Line	Cell type
1	chr3:119011961..119014558-chr3:119015081..119019200,4	MCF-7	breast:
2	chr3:119011699..119014378-chr3:119015999..119019083,3	MCF-7	breast:
3	chr3:119016211..119028042-chr3:119037960..119043695,12	MCF-7	breast:

Variant related genes	Relation type
RPS26P21	TF binding region
ENSG00000031081	Chromatin interaction
ENSG00000241155	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11916079	0.85[EUR][1000 genomes]
rs16829702	0.82[CEU][hapmap]
rs2717260	0.88[CEU][hapmap]
rs4687993	0.88[CEU][hapmap]
rs56007616	0.93[ASN][1000 genomes]
rs56397530	0.84[EUR][1000 genomes]
rs6800377	0.85[EUR][1000 genomes]
rs724653	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7620780	0.94[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[TSI][hapmap]
rs7622994	0.94[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[TSI][hapmap]
rs7623525	0.94[CEU][hapmap]
rs7625392	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs7646428	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9835104	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7640033	IQCB1	cis	cerebellum	SCAN
rs7640033	CD86	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119014200-119017600	Enhancers	Primary T cells from cord blood	blood
2	chr3:119014200-119029800	Weak transcription	Gastric	stomach
3	chr3:119014200-119032800	Weak transcription	Pancreas	Pancrea
4	chr3:119014400-119017400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:119014400-119017600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:119014400-119018000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr3:119014400-119019800	Weak transcription	NHEK	skin
8	chr3:119014400-119021600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:119014400-119021800	Weak transcription	Liver	Liver
10	chr3:119015000-119017400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:119015000-119017800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:119015000-119021800	Weak transcription	Fetal Intestine Large	intestine
13	chr3:119015000-119028600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:119015000-119041200	Weak transcription	Aorta	Aorta
15	chr3:119015200-119020600	Weak transcription	Primary B cells from cord blood	blood
16	chr3:119015200-119021600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:119015200-119041000	Weak transcription	Fetal Kidney	kidney
18	chr3:119015400-119017600	Enhancers	Brain Anterior Caudate	brain
19	chr3:119015400-119017600	Enhancers	Duodenum Mucosa	Duodenum
20	chr3:119015400-119017800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:119015400-119017800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:119015400-119018600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr3:119015400-119019800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:119015400-119019800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:119015600-119017600	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:119015800-119018800	Enhancers	Thymus	Thymus
27	chr3:119015800-119020000	Weak transcription	Colonic Mucosa	Colon
28	chr3:119015800-119024400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:119015800-119024400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:119016000-119017400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr3:119016000-119017400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:119016000-119017400	Enhancers	Ovary	ovary
33	chr3:119016000-119017800	Enhancers	Brain Cingulate Gyrus	brain
34	chr3:119016000-119017800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr3:119016000-119017800	Genic enhancers	Fetal Stomach	stomach
36	chr3:119016000-119021800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:119016000-119035400	Weak transcription	Fetal Brain Male	brain
38	chr3:119016000-119041000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:119016200-119017600	Enhancers	Spleen	Spleen
40	chr3:119016200-119017800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:119016200-119017800	Genic enhancers	HUVEC	blood vessel
42	chr3:119016400-119017400	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:119016400-119017400	Enhancers	Brain Substantia Nigra	brain
44	chr3:119016400-119017400	Genic enhancers	Lung	lung
45	chr3:119016400-119017400	Enhancers	HSMM	muscle
46	chr3:119016400-119017600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:119016400-119017600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:119016400-119017600	Genic enhancers	NH-A	brain
49	chr3:119016400-119017800	Enhancers	Brain Hippocampus Middle	brain
50	chr3:119016400-119017800	Genic enhancers	Fetal Muscle Leg	muscle

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