Variant report

Variant	rs2911589
Chromosome Location	chr1:85034062-85034063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85033825..85035975-chr1:85037159..85040197,3	MCF-7	breast:
2	chr1:84963151..84965022-chr1:85033614..85036547,2	K562	blood:
3	chr1:85015983..85018736-chr1:85033497..85036194,2	K562	blood:
4	chr1:85025088..85026861-chr1:85033231..85035646,2	K562	blood:
5	chr1:84959971..84962240-chr1:85032271..85035203,2	K562	blood:
6	chr1:85022039..85024410-chr1:85033279..85035496,2	K562	blood:

Variant related genes	Relation type
ENSG00000117151	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10874451	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11163969	0.85[EUR][1000 genomes]
rs11163970	0.85[EUR][1000 genomes]
rs11163979	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11163980	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs11163981	0.90[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11163990	0.81[EUR][1000 genomes]
rs11163994	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11163999	0.81[ASN][1000 genomes]
rs1144276	0.80[CHB][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap];0.81[ASN][1000 genomes]
rs12040469	0.81[ASN][1000 genomes]
rs12071149	0.81[CHB][hapmap];0.95[YRI][hapmap];0.81[ASN][1000 genomes]
rs12125418	0.82[EUR][1000 genomes]
rs12128801	0.81[CHB][hapmap];0.88[LWK][hapmap];0.80[MKK][hapmap];0.95[YRI][hapmap]
rs12143652	0.82[CHD][hapmap]
rs12403545	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs1246159	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs1246236	0.81[ASN][1000 genomes]
rs1246253	0.87[CHB][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1246254	1.00[ASW][hapmap];0.85[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1246255	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1400777	0.87[ASW][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1533374	0.81[ASN][1000 genomes]
rs1911159	0.81[CHB][hapmap];0.95[YRI][hapmap]
rs2303306	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303307	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2389743	0.84[ASN][1000 genomes]
rs2659173	0.81[CHB][hapmap];0.95[YRI][hapmap];0.81[ASN][1000 genomes]
rs2677839	0.81[ASN][1000 genomes]
rs2794217	0.81[ASN][1000 genomes]
rs2794218	0.81[CHB][hapmap];0.95[YRI][hapmap];0.81[ASN][1000 genomes]
rs2911588	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2911590	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.97[ASN][1000 genomes]
rs2911591	0.95[ASN][1000 genomes]
rs2911592	0.91[ASN][1000 genomes]
rs2911593	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2911598	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs2911599	0.94[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs2943675	0.95[ASN][1000 genomes]
rs2943676	0.95[ASN][1000 genomes]
rs2943677	0.95[ASN][1000 genomes]
rs2943678	0.91[ASN][1000 genomes]
rs2945146	0.83[ASN][1000 genomes]
rs2945148	0.83[ASN][1000 genomes]
rs2945150	0.89[ASN][1000 genomes]
rs2945152	0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs2945153	0.93[ASN][1000 genomes]
rs2945155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2945158	0.97[ASN][1000 genomes]
rs2945160	0.95[ASN][1000 genomes]
rs2994937	0.80[ASN][1000 genomes]
rs2994940	0.83[ASN][1000 genomes]
rs2994946	0.95[ASN][1000 genomes]
rs2994953	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2994954	0.81[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2994955	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3021402	0.81[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs312397	0.81[CHB][hapmap];0.85[LWK][hapmap];0.95[YRI][hapmap];0.81[ASN][1000 genomes]
rs312401	0.81[ASN][1000 genomes]
rs41299545	0.97[ASN][1000 genomes]
rs4906995	0.90[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs4906997	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4907078	0.89[CEU][hapmap];0.81[CHB][hapmap];0.87[EUR][1000 genomes]
rs4907079	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs6576713	0.81[ASW][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6690204	0.90[CEU][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6692765	0.93[CHB][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6704211	0.81[CHB][hapmap];0.95[YRI][hapmap]
rs7516200	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[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	nsv1000325	chr1:85032605-85100748	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2911589	SPATA1	cis	parietal	SCAN
rs2911589	CTBS	cis	multi-tissue	Pritchard

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84991000-85034200	Weak transcription	Esophagus	oesophagus
2	chr1:84991000-85038200	Weak transcription	Thymus	Thymus
3	chr1:84992400-85038800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr1:84998600-85038800	Weak transcription	Right Ventricle	heart
5	chr1:85001400-85036400	Weak transcription	NH-A	brain
6	chr1:85002000-85038400	Weak transcription	Aorta	Aorta
7	chr1:85002200-85034200	Weak transcription	Lung	lung
8	chr1:85004000-85036400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:85005200-85035000	Weak transcription	Pancreas	Pancrea
10	chr1:85006200-85034600	Weak transcription	Ovary	ovary
11	chr1:85006200-85034800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:85006400-85034400	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:85006600-85038600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:85007200-85038600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:85008800-85039000	Weak transcription	Fetal Brain Male	brain
16	chr1:85009400-85037000	Weak transcription	HUVEC	blood vessel
17	chr1:85014800-85039600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:85016600-85036400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:85017400-85036400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr1:85017400-85039600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:85019200-85038400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:85022000-85038800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:85022400-85034400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:85023400-85034600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:85023400-85036400	Strong transcription	Liver	Liver
26	chr1:85023600-85034200	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:85024000-85035000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr1:85024000-85036200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:85024600-85036400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr1:85024800-85038800	Weak transcription	Brain Angular Gyrus	brain
31	chr1:85025000-85036400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:85025400-85037000	Weak transcription	Small Intestine	intestine
33	chr1:85025600-85038800	Weak transcription	HSMMtube	muscle
34	chr1:85025800-85038800	Weak transcription	Brain Substantia Nigra	brain
35	chr1:85025800-85038800	Weak transcription	Fetal Heart	heart
36	chr1:85026200-85038800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:85026800-85036200	Strong transcription	Primary hematopoietic stem cells	blood
38	chr1:85027000-85035000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:85027200-85035000	Weak transcription	Spleen	Spleen
40	chr1:85027200-85037000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:85027200-85038600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:85027400-85035000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:85027400-85036000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:85027400-85037600	Weak transcription	HepG2	liver
45	chr1:85027800-85038600	Weak transcription	Fetal Kidney	kidney
46	chr1:85028000-85034200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:85028000-85038600	Weak transcription	Fetal Lung	lung
48	chr1:85028200-85037000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:85028200-85038800	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:85028200-85038800	Weak transcription	HSMM	muscle

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