Variant report

Variant	rs2520262
Chromosome Location	chr7:107178382-107178383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1015410	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1018869	0.90[EUR][1000 genomes]
rs1024401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10244871	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10245210	0.81[EUR][1000 genomes]
rs10267425	0.82[AFR][1000 genomes]
rs10267978	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10276321	0.90[EUR][1000 genomes]
rs10953538	0.81[EUR][1000 genomes]
rs11761775	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12532304	0.81[EUR][1000 genomes]
rs12534598	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12668615	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1468335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1858889	0.83[EUR][1000 genomes]
rs2237667	0.91[JPT][hapmap]
rs2250410	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs2253856	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs2283042	0.92[EUR][1000 genomes]
rs2520257	0.93[EUR][1000 genomes]
rs2520258	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2520259	0.96[EUR][1000 genomes]
rs2520266	0.95[EUR][1000 genomes]
rs2520270	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2520272	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2520276	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2520278	0.83[EUR][1000 genomes]
rs2520279	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2701678	0.83[JPT][hapmap]
rs2701679	0.83[JPT][hapmap]
rs2712186	0.95[EUR][1000 genomes]
rs2712188	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2712192	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs2712194	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2712203	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2712213	0.95[EUR][1000 genomes]
rs2712217	0.92[EUR][1000 genomes]
rs2712223	0.94[EUR][1000 genomes]
rs2712225	0.91[EUR][1000 genomes]
rs28410326	0.82[EUR][1000 genomes]
rs3779496	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4610672	0.85[EUR][1000 genomes]
rs4727682	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4730244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs60490203	0.90[EUR][1000 genomes]
rs62483724	0.95[EUR][1000 genomes]
rs6466172	0.93[EUR][1000 genomes]
rs6466174	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6945488	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6962433	0.90[EUR][1000 genomes]
rs6968804	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6979121	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs711442	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7786186	0.83[EUR][1000 genomes]
rs7787113	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs7791955	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs7805630	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1019963	chr7:107033342-107188641	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv539052	chr7:107033342-107188641	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1028571	chr7:107114479-107299723	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv539053	chr7:107114479-107299723	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv482365	chr7:107122401-107271861	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107126800-107184800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr7:107131400-107179800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr7:107144800-107185000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:107146000-107185000	Weak transcription	Brain Hippocampus Middle	brain
5	chr7:107146400-107183800	Weak transcription	Ovary	ovary
6	chr7:107146400-107183800	Weak transcription	Thymus	Thymus
7	chr7:107146400-107184000	Weak transcription	Aorta	Aorta
8	chr7:107147600-107178400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr7:107147600-107183600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr7:107149400-107183800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:107149600-107178800	Weak transcription	Fetal Stomach	stomach
12	chr7:107153800-107183800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr7:107154000-107193800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:107156000-107178400	Weak transcription	Fetal Intestine Large	intestine
15	chr7:107156400-107195000	Weak transcription	Colon Smooth Muscle	Colon
16	chr7:107158000-107183800	Weak transcription	Esophagus	oesophagus
17	chr7:107161000-107185000	Weak transcription	HSMMtube	muscle
18	chr7:107162000-107178600	Weak transcription	Lung	lung
19	chr7:107162000-107184000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr7:107162200-107203400	Weak transcription	Fetal Kidney	kidney
21	chr7:107163000-107184400	Weak transcription	Colonic Mucosa	Colon
22	chr7:107163200-107184600	Weak transcription	NHLF	lung
23	chr7:107163400-107178400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr7:107163400-107184200	Weak transcription	Fetal Thymus	thymus
25	chr7:107163600-107184800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr7:107164200-107185800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr7:107164600-107182800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr7:107164800-107185000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr7:107166600-107194600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr7:107167000-107184400	Weak transcription	Placenta	Placenta
31	chr7:107167200-107178400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:107167200-107178400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr7:107167400-107179800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr7:107167400-107182600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr7:107167400-107183600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr7:107167400-107183800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr7:107167800-107178400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr7:107167800-107183800	Weak transcription	HepG2	liver
39	chr7:107168000-107178400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr7:107168000-107179400	Weak transcription	Adipose Nuclei	Adipose
41	chr7:107168400-107178400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr7:107168600-107184800	Weak transcription	K562	blood
43	chr7:107169400-107178400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr7:107169400-107179200	Weak transcription	HSMM	muscle
45	chr7:107169400-107183600	Weak transcription	HUVEC	blood vessel
46	chr7:107169400-107184400	Weak transcription	NHDF-Ad	bronchial
47	chr7:107169400-107185000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr7:107169400-107185000	Weak transcription	NH-A	brain
49	chr7:107169600-107186400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr7:107169800-107178400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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