Variant report

Variant	rs1962336
Chromosome Location	chr10:50393013-50393014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50392054..50394811-chr10:50506244..50508531,2	K562	blood:

Variant related genes	Relation type
ENSG00000177354	Chromatin interaction
ENSG00000236208	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10776544	0.93[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10857438	0.92[ASN][1000 genomes]
rs10857439	0.83[EUR][1000 genomes]
rs11101006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11101015	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11101016	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12411415	0.80[CHB][hapmap]
rs12570293	0.90[ASN][1000 genomes]
rs12768927	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009325	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17701363	0.93[ASN][1000 genomes]
rs2002332	0.83[ASN][1000 genomes]
rs2377949	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2377994	0.90[ASN][1000 genomes]
rs2377995	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2377996	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2377997	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55908723	0.93[ASN][1000 genomes]
rs61848458	0.93[ASN][1000 genomes]
rs6537507	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7082074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7082708	0.90[JPT][hapmap]
rs7094833	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7475519	0.90[ASN][1000 genomes]
rs7912402	0.83[CEU][hapmap]
rs7922957	0.80[CHB][hapmap]

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	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1962336	ERCC6	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50376800-50395200	Enhancers	Primary B cells from peripheral blood	blood
2	chr10:50381800-50394800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr10:50383400-50395200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr10:50384400-50396000	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr10:50386000-50394800	Weak transcription	Brain Anterior Caudate	brain
6	chr10:50386000-50395200	Weak transcription	Psoas Muscle	Psoas
7	chr10:50386200-50396000	Weak transcription	Placenta	Placenta
8	chr10:50386400-50395200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr10:50386600-50395200	Weak transcription	Lung	lung
10	chr10:50386600-50395200	Weak transcription	Right Ventricle	heart
11	chr10:50386800-50395200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr10:50387000-50394600	Weak transcription	Brain Substantia Nigra	brain
13	chr10:50388400-50394800	Weak transcription	Colonic Mucosa	Colon
14	chr10:50390200-50393200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr10:50390800-50394000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr10:50391000-50393600	Enhancers	Left Ventricle	heart
17	chr10:50391400-50393800	Enhancers	Primary hematopoietic stem cells	blood
18	chr10:50391400-50395400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr10:50391600-50393200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr10:50391600-50393600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr10:50391600-50393600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr10:50391600-50393600	Active TSS	Duodenum Mucosa	Duodenum
23	chr10:50391600-50393600	Enhancers	Fetal Thymus	thymus
24	chr10:50391600-50393600	Flanking Active TSS	Dnd41	blood
25	chr10:50391600-50393600	Flanking Active TSS	K562	blood
26	chr10:50391600-50393800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr10:50391600-50395400	Enhancers	Primary B cells from cord blood	blood
28	chr10:50391600-50399400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr10:50391800-50393200	Enhancers	Primary T cells from cord blood	blood
30	chr10:50392000-50393400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr10:50392000-50393600	Enhancers	GM12878-XiMat	blood
32	chr10:50392000-50395200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr10:50392000-50396000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr10:50392200-50396000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr10:50392400-50393200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr10:50392400-50393600	Enhancers	Brain Hippocampus Middle	brain
37	chr10:50392400-50393600	Enhancers	Fetal Muscle Leg	muscle
38	chr10:50392600-50393200	Enhancers	Fetal Lung	lung
39	chr10:50392600-50393400	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr10:50392600-50394000	Enhancers	Primary T cells fromperipheralblood	blood
41	chr10:50392600-50396000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr10:50392800-50393200	Enhancers	Brain Cingulate Gyrus	brain
43	chr10:50392800-50393200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr10:50392800-50393600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
45	chr10:50392800-50393600	Enhancers	Brain Angular Gyrus	brain
46	chr10:50392800-50393600	Enhancers	Right Atrium	heart
47	chr10:50392800-50393600	Enhancers	Spleen	Spleen
48	chr10:50392800-50396000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr10:50393000-50393200	Active TSS	Rectal Smooth Muscle	rectum
50	chr10:50393000-50393400	Enhancers	Fetal Muscle Trunk	muscle

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