Variant report

Variant	rs10490963
Chromosome Location	chr10:52180423-52180424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr10:52180019-52180432	K562	blood:	n/a	n/a
2	MAZ	chr10:52179977-52180490	K562	blood:	n/a	chr10:52180175-52180185 chr10:52180213-52180222

No.	Distal block	Cell Line	Cell type
1	chr10:52049655..52052352-chr10:52178412..52180723,2	MCF-7	breast:
2	chr10:52175389..52176966-chr10:52179598..52182050,2	K562	blood:
3	chr10:52180307..52183169-chr10:52383906..52386239,2	K562	blood:
4	chr10:52179920..52182656-chr10:52203017..52204731,2	K562	blood:
5	chr10:52179209..52181843-chr10:52226952..52229570,2	MCF-7	breast:
6	chr10:52176749..52178866-chr10:52179847..52182390,3	MCF-7	breast:

Variant related genes	Relation type
SGMS1	TF binding region
ENSG00000198964	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10490964	0.89[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11005626	0.89[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11005959	0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12257419	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12262259	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12411302	1.00[YRI][hapmap]
rs1369860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17438825	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17440448	0.88[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17518471	1.00[ASW][hapmap];0.89[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17519121	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17519380	1.00[ASW][hapmap];0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17721658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17778152	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1916568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1916569	1.00[ASW][hapmap];0.89[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1916571	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2060560	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2064759	0.86[ASW][hapmap];0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs2117961	0.91[ASN][1000 genomes]
rs2117962	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255387	1.00[CHB][hapmap];0.84[JPT][hapmap];0.99[ASN][1000 genomes]
rs2255720	0.99[ASN][1000 genomes]
rs2255849	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2255853	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2255859	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs2574955	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2574956	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2574975	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs2574981	0.99[ASN][1000 genomes]
rs2688875	0.90[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs2688877	0.93[ASN][1000 genomes]
rs2688879	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2842102	0.99[ASN][1000 genomes]
rs2842105	0.99[ASN][1000 genomes]
rs2842106	0.99[ASN][1000 genomes]
rs2842107	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2842109	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3011777	0.84[ASW][hapmap]
rs34672995	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];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34928652	0.92[ASN][1000 genomes]
rs3802537	1.00[ASW][hapmap];0.89[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4935152	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4935673	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4935703	0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4935713	0.87[ASN][1000 genomes]
rs4935729	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55773344	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55861418	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56078228	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56080689	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56133398	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56225400	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56268559	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56277433	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61559519	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61741330	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61856761	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61856763	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61856778	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61856782	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61856787	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61856788	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61856793	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61856794	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61856795	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61856828	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61856832	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61858062	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61858064	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61858065	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61858068	0.89[ASN][1000 genomes]
rs61858069	0.92[ASN][1000 genomes]
rs61858206	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858207	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7067626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7068430	0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs7069115	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082805	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7092753	0.92[ASN][1000 genomes]
rs72801752	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72801754	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72801768	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72801775	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72801776	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72801781	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7392702	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7475420	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7921632	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884880	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	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	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10490963	MSMB	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52178400-52181000	Weak transcription	Esophagus	oesophagus
2	chr10:52178400-52220000	Weak transcription	Pancreas	Pancrea
3	chr10:52178600-52180600	Weak transcription	Primary B cells from cord blood	blood
4	chr10:52178600-52180600	Weak transcription	Brain Anterior Caudate	brain
5	chr10:52178600-52180600	Enhancers	Fetal Intestine Large	intestine
6	chr10:52178600-52180600	Weak transcription	Fetal Kidney	kidney
7	chr10:52178600-52181000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr10:52178600-52181000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr10:52178600-52181000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr10:52178600-52181000	Weak transcription	Brain Angular Gyrus	brain
11	chr10:52178600-52181000	Weak transcription	Psoas Muscle	Psoas
12	chr10:52178600-52181000	Weak transcription	Stomach Mucosa	stomach
13	chr10:52178600-52181000	Weak transcription	Spleen	Spleen
14	chr10:52178600-52181200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr10:52178600-52181400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr10:52178600-52181400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr10:52178600-52181400	Weak transcription	Gastric	stomach
18	chr10:52178600-52181400	Weak transcription	Lung	lung
19	chr10:52178600-52181600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr10:52178600-52181600	Weak transcription	Fetal Stomach	stomach
21	chr10:52178600-52181800	Weak transcription	Fetal Brain Female	brain
22	chr10:52178600-52182000	Enhancers	Brain Hippocampus Middle	brain
23	chr10:52178600-52182400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr10:52178600-52182600	Enhancers	Fetal Lung	lung
25	chr10:52178600-52183400	Enhancers	Brain Cingulate Gyrus	brain
26	chr10:52178600-52188800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr10:52178600-52217200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr10:52178600-52219400	Weak transcription	Left Ventricle	heart
29	chr10:52178800-52180600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr10:52178800-52181000	Weak transcription	Small Intestine	intestine
31	chr10:52178800-52181000	Weak transcription	NHDF-Ad	bronchial
32	chr10:52178800-52181200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr10:52178800-52181600	Enhancers	Brain Substantia Nigra	brain
34	chr10:52178800-52181600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr10:52178800-52182000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr10:52178800-52182400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr10:52178800-52183800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr10:52178800-52187400	Weak transcription	Primary T cells from cord blood	blood
39	chr10:52178800-52191200	Weak transcription	HSMMtube	muscle
40	chr10:52178800-52198000	Weak transcription	Fetal Thymus	thymus
41	chr10:52178800-52202800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr10:52179000-52180600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr10:52179000-52180600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr10:52179000-52181000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr10:52179000-52181600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr10:52179000-52191000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr10:52179000-52191200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr10:52179000-52191400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr10:52179000-52191600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr10:52179000-52205800	Weak transcription	Primary hematopoietic stem cells	blood

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