Variant report

Variant	rs2265195
Chromosome Location	chr10:94082060-94082061
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10748577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10748578	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10748579	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10748580	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10786029	0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs10786033	0.85[EUR][1000 genomes]
rs10786037	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs10882028	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs10882042	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs11186914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11186915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2245994	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2253904	0.88[ASN][1000 genomes]
rs2254667	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2255718	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2488793	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2771248	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[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2771253	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2771256	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2771265	0.85[ASN][1000 genomes]
rs2798254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3781229	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs3824734	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs4933227	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap]
rs4933228	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs4933229	0.84[EUR][1000 genomes]
rs4933720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4999831	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7078559	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs7087501	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs7090737	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7091853	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs7094433	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7908721	0.84[EUR][1000 genomes]
rs7920520	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs855699	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs855702	0.86[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs913649	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs950732	0.82[EUR][1000 genomes]
rs9943333	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv975763	chr10:93822289-94105956	Enhancers Bivalent Enhancer Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1046258	chr10:93866969-94466106	Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2265195	RNLS	cis	parietal	SCAN
rs2265195	RNLS	cis	cerebellum	SCAN
rs2265195	TNKS2	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94052000-94111800	Weak transcription	Gastric	stomach
2	chr10:94052200-94109400	Weak transcription	Esophagus	oesophagus
3	chr10:94052400-94101200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr10:94052400-94101600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr10:94052400-94108800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr10:94052400-94114600	Weak transcription	Colonic Mucosa	Colon
7	chr10:94052600-94102000	Weak transcription	NHLF	lung
8	chr10:94052600-94109400	Weak transcription	HSMMtube	muscle
9	chr10:94052800-94087400	Weak transcription	K562	blood
10	chr10:94052800-94088600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr10:94053200-94086800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr10:94053400-94109400	Weak transcription	Fetal Brain Male	brain
13	chr10:94054600-94101400	Weak transcription	HSMM	muscle
14	chr10:94054800-94087200	Weak transcription	NHEK	skin
15	chr10:94056800-94087600	Weak transcription	A549	lung
16	chr10:94063600-94109400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr10:94063600-94111800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr10:94064000-94087600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr10:94064000-94087800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr10:94064000-94101400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr10:94064000-94109200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr10:94064200-94086400	Weak transcription	Fetal Heart	heart
23	chr10:94065800-94093000	Weak transcription	Psoas Muscle	Psoas
24	chr10:94066000-94087400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr10:94066200-94101600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr10:94067000-94082800	Weak transcription	Pancreas	Pancrea
27	chr10:94067000-94089600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr10:94067000-94113400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr10:94068400-94087600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr10:94068600-94089800	Weak transcription	Small Intestine	intestine
31	chr10:94070800-94094800	Weak transcription	Colon Smooth Muscle	Colon
32	chr10:94071800-94108200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr10:94072000-94086800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr10:94072000-94102200	Weak transcription	NHDF-Ad	bronchial
35	chr10:94072200-94087200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr10:94072200-94088000	Weak transcription	HUVEC	blood vessel
37	chr10:94072200-94109000	Weak transcription	Brain Anterior Caudate	brain
38	chr10:94072200-94109400	Weak transcription	Aorta	Aorta
39	chr10:94072400-94089800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr10:94072400-94101600	Weak transcription	NH-A	brain
41	chr10:94072600-94087200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr10:94072600-94087200	Weak transcription	HMEC	breast
43	chr10:94072600-94094800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr10:94072800-94086400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr10:94072800-94087400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr10:94072800-94101200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr10:94073000-94087200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr10:94073000-94087400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr10:94073000-94090000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr10:94073000-94101800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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