Variant report

Variant	rs3011710
Chromosome Location	chr10:52348894-52348895
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:52287492..52289090-chr10:52346967..52349226,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10763584	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10763585	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10826234	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11006119	0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs11006155	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12358162	0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs1884571	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs2208036	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2860472	0.88[JPT][hapmap]
rs2983360	0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs2983364	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3011707	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3011802	0.87[ASN][1000 genomes]
rs3920545	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.96[ASN][1000 genomes]
rs55735989	0.80[ASN][1000 genomes]
rs6481433	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7074405	0.92[ASN][1000 genomes]
rs7075104	0.93[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7088807	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7898315	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
7	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3011710	MSMB	cis	parietal	SCAN
rs3011710	PIK3C2B	trans	parietal	SCAN
rs3011710	PARG	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52336200-52349000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr10:52336800-52363000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr10:52337800-52352800	Weak transcription	Fetal Brain Male	brain
4	chr10:52338000-52356400	Weak transcription	Fetal Brain Female	brain
5	chr10:52338000-52363800	Weak transcription	Fetal Kidney	kidney
6	chr10:52338000-52367000	Weak transcription	Aorta	Aorta
7	chr10:52338200-52353600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr10:52338200-52353800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr10:52338600-52353400	Weak transcription	Brain Germinal Matrix	brain
10	chr10:52338600-52353600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr10:52340400-52360200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:52341200-52373000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr10:52341400-52355400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr10:52341400-52360200	Weak transcription	GM12878-XiMat	blood
15	chr10:52341800-52350600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr10:52341800-52351800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr10:52341800-52352800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr10:52341800-52355000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:52341800-52362000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr10:52342000-52352000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr10:52342200-52351800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr10:52342400-52351600	Weak transcription	Brain Angular Gyrus	brain
23	chr10:52342400-52353000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr10:52342600-52356400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr10:52342800-52360200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr10:52343000-52349000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr10:52343000-52353000	Weak transcription	Fetal Heart	heart
28	chr10:52343400-52360600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr10:52343600-52356200	Weak transcription	Stomach Mucosa	stomach
30	chr10:52343600-52362200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr10:52343800-52360000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr10:52344400-52349800	Strong transcription	Primary B cells from cord blood	blood
33	chr10:52345000-52350000	Strong transcription	Primary T cells from cord blood	blood
34	chr10:52345000-52353000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr10:52346000-52349600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr10:52346000-52349600	Strong transcription	Ovary	ovary
37	chr10:52346000-52355400	Weak transcription	Colon Smooth Muscle	Colon
38	chr10:52346200-52349400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr10:52346200-52349600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr10:52346200-52350000	Strong transcription	Primary B cells from peripheral blood	blood
41	chr10:52346400-52349600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr10:52346400-52358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr10:52346600-52349000	Weak transcription	Brain Substantia Nigra	brain
44	chr10:52346600-52349000	Weak transcription	Gastric	stomach
45	chr10:52346600-52349000	Weak transcription	Left Ventricle	heart
46	chr10:52346600-52350600	Weak transcription	Pancreas	Pancrea
47	chr10:52346600-52351000	Weak transcription	Right Ventricle	heart
48	chr10:52346600-52351800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr10:52346600-52351800	Weak transcription	Right Atrium	heart
50	chr10:52346600-52352600	Weak transcription	HSMMtube	muscle

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