Variant report

Variant	rs9430635
Chromosome Location	chr1:9738786-9738787
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9734041..9735853-chr1:9737561..9739742,2	MCF-7	breast:
2	chr1:9736879..9743204-chr1:9743811..9749171,7	K562	blood:

Variant related genes	Relation type
ENSG00000171608	Chromatin interaction
ENSG00000231789	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12568084	0.81[ASN][1000 genomes]
rs4240910	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs4333853	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4420084	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4488033	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4601595	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4846192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4846194	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56338585	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6660363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6669509	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9430636	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9430640	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9430641	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9430648	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9430635	PIK3CD	cis	parietal	SCAN
rs9430635	RPL22	cis	cerebellum	SCAN
rs9430635	SRM	cis	cerebellum	SCAN
rs9430635	NMNAT1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9713200-9744000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:9713200-9747200	Weak transcription	Pancreas	Pancrea
3	chr1:9714000-9739600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:9727200-9741000	Strong transcription	Dnd41	blood
5	chr1:9729600-9746800	Weak transcription	Thymus	Thymus
6	chr1:9730800-9740000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:9731000-9739600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr1:9732400-9741800	Weak transcription	A549	lung
9	chr1:9732600-9743800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:9734400-9741800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:9734600-9743600	Weak transcription	Fetal Thymus	thymus
12	chr1:9735400-9739000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:9735400-9742000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:9735600-9741000	Genic enhancers	Primary B cells from peripheral blood	blood
15	chr1:9735600-9744200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:9735800-9744200	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr1:9736200-9741200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr1:9736400-9739000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:9736400-9740400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:9736800-9741000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:9737000-9739200	Strong transcription	Primary T cells from cord blood	blood
22	chr1:9737000-9740600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:9737200-9740400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:9737200-9740600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:9737200-9740800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:9737400-9739600	Weak transcription	Spleen	Spleen
27	chr1:9737400-9744400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:9737400-9745800	Weak transcription	K562	blood
29	chr1:9737400-9747000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:9737400-9747200	Weak transcription	Right Atrium	heart
31	chr1:9737600-9741000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:9738200-9741200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:9738200-9746000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:9738400-9739600	Strong transcription	Primary B cells from cord blood	blood
35	chr1:9738400-9739800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:9738600-9738800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr1:9738600-9738800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr1:9738600-9739200	Genic enhancers	GM12878-XiMat	blood
39	chr1:9738600-9741200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:9738600-9742000	Enhancers	Primary T killer memory cells from peripheral blood	blood

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