Variant report

Variant	rs2092996
Chromosome Location	chr10:52281609-52281610
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:52272629..52275165-chr10:52281578..52283752,2	K562	blood:
2	chr10:52279739..52282600-chr10:52286239..52288790,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1011881	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10740714	0.88[EUR][1000 genomes]
rs10763529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826100	0.91[JPT][hapmap]
rs10826118	0.88[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10826126	0.92[CEU][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11005937	0.90[EUR][1000 genomes]
rs1203413	0.81[JPT][hapmap]
rs1203415	0.86[JPT][hapmap]
rs12356922	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1548256	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1569962	0.88[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs1569963	0.88[EUR][1000 genomes]
rs1810576	0.82[EUR][1000 genomes]
rs1916566	0.86[JPT][hapmap]
rs2099527	0.86[JPT][hapmap]
rs2144862	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2339505	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2339506	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2574959	0.81[JPT][hapmap]
rs2842103	0.81[JPT][hapmap]
rs4312019	0.81[JPT][hapmap]
rs4935712	0.88[CEU][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4935727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4935730	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7071603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7075289	0.92[CEU][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7904833	0.91[JPT][hapmap]
rs978588	0.88[CEU][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv895391	chr10:52260398-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv895392	chr10:52263910-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv467193	chr10:52265265-52289664	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv550855	chr10:52265265-52289664	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2092996	ERCC6	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52262200-52287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr10:52266800-52282400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:52267000-52282400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr10:52268200-52282400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr10:52268200-52282600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr10:52268400-52282200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr10:52270000-52282400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr10:52270000-52282800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr10:52270200-52282600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:52271200-52283000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr10:52271600-52300600	Weak transcription	Aorta	Aorta
12	chr10:52272400-52284600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr10:52272600-52302800	Weak transcription	Fetal Stomach	stomach
14	chr10:52272800-52288200	Weak transcription	HSMMtube	muscle
15	chr10:52273200-52282600	Weak transcription	Right Ventricle	heart
16	chr10:52273200-52285800	Weak transcription	K562	blood
17	chr10:52273200-52287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr10:52273200-52287400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr10:52273200-52288400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr10:52273400-52282600	Weak transcription	Thymus	Thymus
21	chr10:52273400-52282800	Weak transcription	Spleen	Spleen
22	chr10:52273400-52283800	Weak transcription	Fetal Thymus	thymus
23	chr10:52273400-52286000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr10:52273400-52287000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr10:52273400-52287200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr10:52273600-52286800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr10:52273600-52287400	Weak transcription	GM12878-XiMat	blood
28	chr10:52273600-52289600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr10:52273600-52298400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr10:52273600-52299800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr10:52273800-52282400	Weak transcription	Primary T cells from cord blood	blood
32	chr10:52274000-52282200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr10:52274000-52287200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr10:52274800-52288200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr10:52275200-52294200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr10:52275600-52282600	Weak transcription	Esophagus	oesophagus
37	chr10:52275600-52285000	Weak transcription	Gastric	stomach
38	chr10:52275600-52286800	Weak transcription	Pancreas	Pancrea
39	chr10:52276200-52282600	Weak transcription	Right Atrium	heart
40	chr10:52276200-52286200	Weak transcription	Fetal Heart	heart
41	chr10:52276800-52282400	Weak transcription	Psoas Muscle	Psoas
42	chr10:52277000-52282400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr10:52277600-52282600	Weak transcription	Fetal Lung	lung
44	chr10:52277600-52282800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr10:52277800-52282600	Weak transcription	Brain Anterior Caudate	brain
46	chr10:52277800-52283000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr10:52278000-52282400	Weak transcription	Brain Angular Gyrus	brain
48	chr10:52278000-52282400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr10:52279400-52282400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr10:52279400-52282400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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