Variant report

Variant	rs7869421
Chromosome Location	chr9:95749905-95749906
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95749653..95752531-chr9:95761934..95764790,2	MCF-7	breast:
2	chr9:95735773..95738938-chr9:95746079..95753670,13	MCF-7	breast:
3	chr9:95746898..95754225-chr9:95890814..95897960,9	MCF-7	breast:
4	chr9:95749058..95750589-chr9:95762192..95765185,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127084	Chromatin interaction
ENSG00000131669	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10121856	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10283714	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739940	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10761189	0.95[JPT][hapmap]
rs10821046	0.90[GIH][hapmap]
rs10821048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10821049	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821050	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821051	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992561	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992564	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11788120	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13300085	0.95[JPT][hapmap]
rs3802381	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3936099	0.90[GIH][hapmap]
rs4302906	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744159	0.87[EUR][1000 genomes]
rs4744161	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6479445	0.95[JPT][hapmap]
rs7026624	0.95[GIH][hapmap]
rs7030160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7032953	0.82[EUR][1000 genomes]
rs7847879	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7848528	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7850247	0.82[CEU][hapmap]
rs7867742	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7869056	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7870077	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7875497	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9942903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9942965	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Strong transcription 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	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7869421	SUSD3	cis	multi-tissue	Pritchard
rs7869421	ZNF484	cis	cerebellum	SCAN
rs7869421	ZNF484	cis	parietal	SCAN
rs7869421	FGD3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95735400-95752600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
2	chr9:95740000-95754800	Weak transcription	Gastric	stomach
3	chr9:95740000-95754800	Weak transcription	Pancreas	Pancrea
4	chr9:95740200-95750000	Weak transcription	Esophagus	oesophagus
5	chr9:95740200-95750600	Weak transcription	Lung	lung
6	chr9:95744400-95751400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr9:95745800-95753200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr9:95746200-95751400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr9:95746400-95751000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr9:95746400-95752600	Genic enhancers	Primary T cells from cord blood	blood
11	chr9:95746600-95750000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr9:95746600-95750200	Strong transcription	Primary hematopoietic stem cells	blood
13	chr9:95746600-95752000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr9:95747000-95752200	Genic enhancers	Primary T cells fromperipheralblood	blood
15	chr9:95747200-95750600	Genic enhancers	Primary B cells from peripheral blood	blood
16	chr9:95747200-95752600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:95747600-95750400	Strong transcription	Primary B cells from cord blood	blood
18	chr9:95747600-95750400	Weak transcription	GM12878-XiMat	blood
19	chr9:95747600-95751400	Strong transcription	Dnd41	blood
20	chr9:95747800-95754600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr9:95748000-95750600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr9:95748200-95756000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
23	chr9:95748400-95751200	Enhancers	Placenta	Placenta
24	chr9:95748600-95750400	Weak transcription	Fetal Brain Female	brain
25	chr9:95748800-95750000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:95748800-95750000	Strong transcription	Thymus	Thymus
27	chr9:95748800-95750600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr9:95749000-95750400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:95749000-95750400	Weak transcription	Hela-S3	cervix
30	chr9:95749000-95751800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:95749000-95752800	Enhancers	HepG2	liver
32	chr9:95749200-95750200	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr9:95749200-95750400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:95749200-95750600	Weak transcription	Fetal Intestine Large	intestine
35	chr9:95749200-95752000	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr9:95749200-95755600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr9:95749400-95750200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
38	chr9:95749800-95750000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:95749800-95750200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr9:95749800-95750600	Enhancers	Spleen	Spleen
41	chr9:95749800-95751200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
42	chr9:95749800-95751200	Genic enhancers	Fetal Thymus	thymus
43	chr9:95749800-95751400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
44	chr9:95749800-95751400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr9:95749800-95751400	ZNF genes & repeats	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links