Variant report

Variant	rs312397
Chromosome Location	chr1:84973434-84973435
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	IRF1	chr1:84971683-84973686	K562	blood:	n/a	chr1:84973663-84973677 chr1:84972218-84972230 chr1:84973666-84973678 chr1:84972255-84972264
2	POLR2A	chr1:84957385-84973725	K562	blood:	n/a	n/a
3	RCOR1	chr1:84973101-84973756	K562	blood:	n/a	n/a
4	EP300	chr1:84973218-84973716	K562	blood:	n/a	n/a
5	MYC	chr1:84973355-84973638	K562	blood:	n/a	n/a
6	TBL1XR1	chr1:84971865-84973452	K562	blood:	n/a	n/a
7	IRF1	chr1:84971787-84973563	K562	blood:	n/a	chr1:84972218-84972230 chr1:84972255-84972264
8	ZNF384	chr1:84973416-84974018	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:84972325..84974748-chr1:85028304..85030920,3	K562	blood:
2	chr1:84969735..84979623-chr1:84983174..84994888,16	K562	blood:
3	chr1:84973180..84975531-chr1:85217909..85219916,2	K562	blood:
4	chr1:84973183..84975597-chr1:85046521..85049495,2	K562	blood:
5	chr1:84972312..84973826-chr1:85135487..85137593,2	K562	blood:
6	chr1:84970994..84973830-chr1:85154472..85157447,5	K562	blood:
7	chr1:84966614..84978118-chr1:85034515..85041986,38	K562	blood:
8	chr1:84966967..84974535-chr1:85036439..85041823,24	K562	blood:

Variant related genes	Relation type
GNG5	TF binding region
ENSG00000117151	Chromatin interaction
ENSG00000117155	Chromatin interaction
ENSG00000122432	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11163969	0.94[ASN][1000 genomes]
rs11163970	0.94[ASN][1000 genomes]
rs11163971	0.81[CHB][hapmap]
rs11163972	0.81[CHB][hapmap]
rs11163979	1.00[ASN][1000 genomes]
rs11163980	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163981	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs11163990	0.96[ASN][1000 genomes]
rs11163994	1.00[ASN][1000 genomes]
rs11163999	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1123981	0.81[CHB][hapmap]
rs1144276	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586006	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs12036957	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12040469	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12071149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124731	0.81[CHB][hapmap]
rs12126584	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs12126924	0.81[CHB][hapmap]
rs12128801	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12136756	0.81[CHB][hapmap]
rs12403545	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1246159	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1246236	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1246253	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1246254	0.94[CHB][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs1246255	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1400777	0.86[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1506707	0.81[CHB][hapmap]
rs1533374	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110519	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs1911159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2271620	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs2292191	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303306	0.81[CHB][hapmap];0.95[YRI][hapmap];0.81[ASN][1000 genomes]
rs2389743	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2677839	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794217	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2911589	0.81[CHB][hapmap];0.85[LWK][hapmap];0.95[YRI][hapmap];0.81[ASN][1000 genomes]
rs2911590	0.86[ASW][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap]
rs2911593	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2945152	0.86[ASW][hapmap]
rs2945155	0.81[CHB][hapmap]
rs2994953	0.81[CHB][hapmap]
rs2994954	0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs2994955	0.88[ASN][1000 genomes]
rs3021402	0.94[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs312395	0.81[CHB][hapmap]
rs312401	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813605	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs4906995	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4906997	0.87[ASN][1000 genomes]
rs4907076	0.84[CHD][hapmap]
rs4907078	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6576713	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6576715	0.82[ASN][1000 genomes]
rs6690204	0.81[TSI][hapmap]
rs6692765	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6704211	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7512922	0.81[CHB][hapmap]
rs7514763	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs7516200	0.92[ASN][1000 genomes]
rs7519606	0.81[CHB][hapmap]
rs7537818	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9645393	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs312397	SPATA1	cis	parietal	SCAN
rs312397	BCL10	cis	cerebellum	SCAN
rs312397	CTBS	cis	multi-tissue	Pritchard

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84970000-84973600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:84970000-84973600	Active TSS	GM12878-XiMat	blood
3	chr1:84970000-84973600	Active TSS	NHLF	lung
4	chr1:84970400-84973600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:84970400-84973600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:84970400-84973600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:84970400-84973600	Active TSS	A549	lung
8	chr1:84970800-84973600	Active TSS	K562	blood
9	chr1:84972600-84973600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr1:84972600-84973600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:84972600-84975200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:84972600-84975200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:84972800-84973600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:84972800-84973600	Flanking Active TSS	Dnd41	blood
15	chr1:84973000-84973600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:84973000-84973600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:84973000-84973600	Enhancers	Fetal Brain Female	brain
18	chr1:84973000-84973600	Weak transcription	Fetal Stomach	stomach
19	chr1:84973000-84973600	Weak transcription	Left Ventricle	heart
20	chr1:84973000-84974000	Enhancers	Aorta	Aorta
21	chr1:84973000-84974600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:84973000-84974600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:84973000-84975200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:84973000-84976200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:84973000-84977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:84973000-85003200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:84973200-84973600	Enhancers	Liver	Liver
28	chr1:84973200-84973600	Enhancers	Fetal Intestine Small	intestine
29	chr1:84973200-84973600	Enhancers	Hela-S3	cervix
30	chr1:84973200-84973800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:84973200-84973800	Flanking Active TSS	HepG2	liver
32	chr1:84973200-84974200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:84973200-84974400	Enhancers	Fetal Intestine Large	intestine
34	chr1:84973200-84975000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:84973200-84982200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:84973200-84982200	Weak transcription	NHDF-Ad	bronchial
37	chr1:84973200-85003200	Weak transcription	Adipose Nuclei	Adipose
38	chr1:84973400-84973600	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr1:84973400-84973600	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr1:84973400-84973600	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr1:84973400-84973600	Enhancers	Fetal Heart	heart
42	chr1:84973400-84973800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:84973400-84973800	Enhancers	Primary hematopoietic stem cells	blood
44	chr1:84973400-84973800	Enhancers	Fetal Thymus	thymus
45	chr1:84973400-84973800	Enhancers	Right Atrium	heart
46	chr1:84973400-84973800	Flanking Active TSS	Thymus	Thymus
47	chr1:84973400-84974200	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr1:84973400-84976000	Weak transcription	HUVEC	blood vessel
49	chr1:84973400-84991600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:84973400-84993800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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