Variant report

Variant	rs11586006
Chromosome Location	chr1:84973205-84973206
allele	A/G
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	MXI1	chr1:84969756-84973236	IMR90	lung:	n/a	n/a
3	POLR2A	chr1:84957385-84973725	K562	blood:	n/a	n/a
4	RCOR1	chr1:84973101-84973756	K562	blood:	n/a	n/a
5	TBL1XR1	chr1:84971865-84973452	K562	blood:	n/a	n/a
6	TAL1	chr1:84971710-84973268	K562	blood:	n/a	n/a
7	ARID3A	chr1:84971737-84973402	HepG2	liver:	n/a	n/a
8	IRF1	chr1:84971787-84973563	K562	blood:	n/a	chr1:84972218-84972230 chr1:84972255-84972264
9	POLR2A	chr1:84968805-84973213	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:84970263-84973254	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:84944684..84947410-chr1:84970225..84973395,6	MCF-7	breast:
2	chr1:84972325..84974748-chr1:85028304..85030920,3	K562	blood:
3	chr1:84969735..84979623-chr1:84983174..84994888,16	K562	blood:
4	chr1:84973180..84975531-chr1:85217909..85219916,2	K562	blood:
5	chr1:84973183..84975597-chr1:85046521..85049495,2	K562	blood:
6	chr1:84972312..84973826-chr1:85135487..85137593,2	K562	blood:
7	chr1:84970994..84973830-chr1:85154472..85157447,5	K562	blood:
8	chr1:84966614..84978118-chr1:85034515..85041986,38	K562	blood:
9	chr1:84966967..84974535-chr1:85036439..85041823,24	K562	blood:

Variant related genes	Relation type
GNG5	TF binding region
ENSG00000122432	Chromatin interaction
ENSG00000117151	Chromatin interaction
ENSG00000117133	Chromatin interaction
ENSG00000117155	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11163971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11163972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11163980	0.81[CHB][hapmap]
rs11163981	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs11163992	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1123981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144276	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs11578494	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12071149	0.81[CHB][hapmap]
rs12123381	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124568	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12126584	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128801	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs12136756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140555	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143652	0.93[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12145405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1246159	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs1395416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17109982	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17110030	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17110519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1911159	0.81[CHB][hapmap]
rs2271620	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292191	0.84[CHD][hapmap]
rs2292808	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659173	0.81[CHB][hapmap]
rs2794218	0.81[CHB][hapmap]
rs312395	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs312397	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs3813605	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813607	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3922538	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4906995	0.81[CHB][hapmap]
rs4907076	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4907077	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4907078	0.81[CHB][hapmap]
rs56212819	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57245302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57442052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704211	0.81[CHB][hapmap]
rs74095416	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74095424	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74095432	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74095436	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7519606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7535445	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7536988	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs925740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs11586006	SPATA1	cis	parietal	SCAN
rs11586006	SPATA1	cis	multi-tissue	Pritchard
rs11586006	ZSWIM1	trans	cerebellum	SCAN

Chromatin state (count:60 , 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	chr1:84970200-84973400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:84970200-84973400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:84970400-84973400	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr1:84970400-84973600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:84970400-84973600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:84970400-84973600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:84970400-84973600	Active TSS	A549	lung
11	chr1:84970800-84973600	Active TSS	K562	blood
12	chr1:84972600-84973400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:84972600-84973400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr1:84972600-84973400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:84972600-84973600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr1:84972600-84973600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:84972600-84975200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:84972600-84975200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:84972800-84973400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr1:84972800-84973400	Flanking Active TSS	HUVEC	blood vessel
21	chr1:84972800-84973400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr1:84972800-84973600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:84972800-84973600	Flanking Active TSS	Dnd41	blood
24	chr1:84973000-84973400	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr1:84973000-84973400	Flanking Active TSS	Fetal Heart	heart
26	chr1:84973000-84973400	Enhancers	Fetal Lung	lung
27	chr1:84973000-84973600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:84973000-84973600	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:84973000-84973600	Enhancers	Fetal Brain Female	brain
30	chr1:84973000-84973600	Weak transcription	Fetal Stomach	stomach
31	chr1:84973000-84973600	Weak transcription	Left Ventricle	heart
32	chr1:84973000-84974000	Enhancers	Aorta	Aorta
33	chr1:84973000-84974600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:84973000-84974600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:84973000-84975200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:84973000-84976200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:84973000-84977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr1:84973000-85003200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:84973200-84973400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr1:84973200-84973400	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr1:84973200-84973400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr1:84973200-84973400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:84973200-84973400	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr1:84973200-84973400	Enhancers	Primary B cells from cord blood	blood
45	chr1:84973200-84973400	Enhancers	Primary T cells from cord blood	blood
46	chr1:84973200-84973400	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr1:84973200-84973400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr1:84973200-84973400	Active TSS	Thymus	Thymus
49	chr1:84973200-84973400	Enhancers	Osteobl	bone
50	chr1:84973200-84973600	Enhancers	Liver	Liver

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