Variant report

Variant	rs2994953
Chromosome Location	chr1:85031630-85031631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:85022443..85024942-chr1:85030020..85032118,2	K562	blood:
2	chr1:84963450..84965371-chr1:85030110..85032846,2	K562	blood:
3	chr1:85022443..85025192-chr1:85030374..85032118,2	K562	blood:
4	chr1:85030646..85033107-chr1:85038091..85041262,3	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPF1-1	chr1:85031544-85031875	NONHSAT004204
2	lnc-RPF1-1	chr1:85031544-85031877	NONHSAT004212
3	lnc-CTBS-1	chr1:85031524-85031695	NONHSAT004214
4	lnc-RPF1-1	chr1:85031544-85032789	NONHSAT004213

No data

Variant related genes	Relation type
ENSG00000117151	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11163980	0.81[CHB][hapmap]
rs11163981	0.81[CHB][hapmap]
rs11164004	0.80[EUR][1000 genomes]
rs1144276	0.80[CHB][hapmap]
rs12071149	0.81[CHB][hapmap]
rs12125418	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs12128801	0.81[CHB][hapmap]
rs12143652	0.82[CHD][hapmap];0.85[GIH][hapmap];0.80[EUR][1000 genomes]
rs12403545	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs1246159	0.81[CHB][hapmap]
rs1246253	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs1246254	0.87[CHB][hapmap];0.97[CHD][hapmap];0.82[ASN][1000 genomes]
rs1246255	0.80[ASN][1000 genomes]
rs1400777	0.86[CHB][hapmap];0.97[CHD][hapmap];0.82[ASN][1000 genomes]
rs1517602	0.81[EUR][1000 genomes]
rs15911	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs17374941	0.82[EUR][1000 genomes]
rs1911159	0.81[CHB][hapmap]
rs2303306	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303307	0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2389743	0.80[ASN][1000 genomes]
rs2659173	0.81[CHB][hapmap]
rs2794218	0.81[CHB][hapmap]
rs2911588	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2911589	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]
rs2911590	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2911591	0.91[ASN][1000 genomes]
rs2911592	0.95[ASN][1000 genomes]
rs2911593	0.82[ASN][1000 genomes]
rs2911598	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs2911599	0.94[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs2943675	0.91[ASN][1000 genomes]
rs2943676	0.91[ASN][1000 genomes]
rs2943677	0.91[ASN][1000 genomes]
rs2943678	0.95[ASN][1000 genomes]
rs2945145	0.89[MEX][hapmap]
rs2945147	0.83[MEX][hapmap]
rs2945150	0.85[ASN][1000 genomes]
rs2945152	0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2945153	0.97[ASN][1000 genomes]
rs2945155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2945158	0.93[ASN][1000 genomes]
rs2945160	0.91[ASN][1000 genomes]
rs2994937	0.84[ASN][1000 genomes]
rs2994946	0.91[ASN][1000 genomes]
rs2994954	0.90[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2994955	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3021402	0.89[ASW][hapmap];0.90[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs312397	0.81[CHB][hapmap]
rs41299545	0.93[ASN][1000 genomes]
rs4906995	0.81[CHB][hapmap]
rs4906997	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4907078	0.89[CEU][hapmap];0.81[CHB][hapmap]
rs4907080	0.81[EUR][1000 genomes]
rs6576713	0.87[CHB][hapmap];0.97[CHD][hapmap];0.80[ASN][1000 genomes]
rs6692765	0.93[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs6704211	0.81[CHB][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2994953	SPATA1	cis	parietal	SCAN
rs2994953	CTBS	cis	multi-tissue	Pritchard

Chromatin state (count:102 , 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	chr1:85001600-85033600	Weak transcription	NHLF	lung
7	chr1:85002000-85038400	Weak transcription	Aorta	Aorta
8	chr1:85002200-85034200	Weak transcription	Lung	lung
9	chr1:85003800-85033600	Weak transcription	Left Ventricle	heart
10	chr1:85004000-85036400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:85005200-85035000	Weak transcription	Pancreas	Pancrea
12	chr1:85006200-85034600	Weak transcription	Ovary	ovary
13	chr1:85006200-85034800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:85006400-85034400	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:85006600-85038600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:85007200-85038600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:85008800-85039000	Weak transcription	Fetal Brain Male	brain
18	chr1:85009400-85037000	Weak transcription	HUVEC	blood vessel
19	chr1:85014800-85039600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:85016600-85036400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr1:85017400-85036400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:85017400-85039600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:85019200-85038400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:85019400-85032200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:85022000-85038800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:85022400-85034400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:85023400-85034600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:85023400-85036400	Strong transcription	Liver	Liver
29	chr1:85023600-85034200	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:85024000-85035000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr1:85024000-85036200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:85024200-85033400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:85024600-85032000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:85024600-85036400	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr1:85024800-85038800	Weak transcription	Brain Angular Gyrus	brain
36	chr1:85025000-85036400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:85025400-85037000	Weak transcription	Small Intestine	intestine
38	chr1:85025600-85038800	Weak transcription	HSMMtube	muscle
39	chr1:85025800-85038800	Weak transcription	Brain Substantia Nigra	brain
40	chr1:85025800-85038800	Weak transcription	Fetal Heart	heart
41	chr1:85026200-85032200	Strong transcription	Primary B cells from cord blood	blood
42	chr1:85026200-85038800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:85026800-85032000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:85026800-85036200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr1:85027000-85035000	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr1:85027200-85032600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:85027200-85035000	Weak transcription	Spleen	Spleen
48	chr1:85027200-85037000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:85027200-85038600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:85027400-85035000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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