Variant report

Variant	rs1203418
Chromosome Location	chr10:52178587-52178588
allele	A/G
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	GATA1	chr10:52177492-52178656	PBDE	blood:	n/a	n/a
2	IRF1	chr10:52177496-52178676	K562	blood:	n/a	chr10:52178455-52178469 chr10:52178456-52178466 chr10:52178237-52178246 chr10:52177524-52177535 chr10:52178455-52178469
3	POLR2A	chr10:52177300-52178652	GM19193	blood:	n/a	n/a
4	TCF12	chr10:52177526-52178705	A549	lung:	n/a	n/a
5	SP1	chr10:52177928-52178604	A549	lung:	n/a	chr10:52178258-52178279
6	POLR2A	chr10:52177337-52178609	Hela-S3	cervix:	n/a	n/a
7	EP300	chr10:52178050-52178670	A549	lung:	n/a	chr10:52178229-52178243
8	POLR2A	chr10:52177259-52178635	GM18951	blood:	n/a	n/a
9	POLR2A	chr10:52177318-52179054	GM19099	blood:	n/a	n/a
10	POLR2A	chr10:52177323-52178618	Raji	blood:	n/a	n/a
11	IRF1	chr10:52178013-52178932	K562	blood:	n/a	chr10:52178455-52178469 chr10:52178456-52178466 chr10:52178237-52178246 chr10:52178455-52178469
12	MAX	chr10:52177184-52178611	A549	lung:	n/a	chr10:52177324-52177335 chr10:52178237-52178246
13	POLR2A	chr10:52177657-52178600	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr10:52177161-52178587	Hela-S3	cervix:	n/a	n/a
15	RCOR1	chr10:52177260-52178913	IMR90	lung:	n/a	n/a
16	POLR2A	chr10:52177339-52178657	GM12891	blood:	n/a	n/a
17	POLR2A	chr10:52177221-52178609	GM12892	blood:	n/a	n/a
18	WRNIP1	chr10:52178404-52178629	GM12878	blood:	n/a	n/a
19	POLR2A	chr10:52177251-52178600	GM12878	blood:	n/a	n/a
20	NFYB	chr10:52178079-52178614	K562	blood:	n/a	chr10:52178254-52178269 chr10:52178257-52178271 chr10:52178257-52178272 chr10:52178257-52178272 chr10:52178259-52178269
21	MAZ	chr10:52177717-52178678	K562	blood:	n/a	chr10:52178237-52178246
22	POLR2A	chr10:52177293-52179162	MCF10A-Er-Src	breast:	n/a	n/a
23	JUN	chr10:52177813-52178692	K562	blood:	n/a	chr10:52178236-52178248 chr10:52178238-52178246 chr10:52178237-52178247 chr10:52178237-52178247 chr10:52178078-52178087
24	POLR2A	chr10:52177299-52178606	GM12892	blood:	n/a	n/a
25	POLR2A	chr10:52177278-52178693	PBDE	blood:	n/a	n/a
26	POLR2A	chr10:52177743-52178643	U87	brain:	n/a	n/a
27	POLR2A	chr10:52177266-52178615	GM18505	blood:	n/a	n/a
28	POLR2A	chr10:52176699-52178672	GM12878	blood:	n/a	n/a
29	NFYB	chr10:52178058-52178650	GM12878	blood:	n/a	chr10:52178254-52178269 chr10:52178257-52178271 chr10:52178257-52178272 chr10:52178257-52178272 chr10:52178259-52178269
30	POLR2A	chr10:52177749-52178637	U87	brain:	n/a	n/a
31	RELA	chr10:52177312-52178602	GM19099	blood:	n/a	n/a
32	POLR2A	chr10:52177187-52178664	GM12892	blood:	n/a	n/a
33	POLR2A	chr10:52177123-52178620	GM12878	blood:	n/a	n/a
34	POLR2A	chr10:52176070-52179101	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:52176233..52179172-chr10:52229395..52232901,6	MCF-7	breast:
2	chr10:52173595..52180106-chr10:52381535..52385847,7	MCF-7	breast:
3	chr10:52049655..52052352-chr10:52178412..52180723,2	MCF-7	breast:
4	chr10:52173619..52179913-chr10:52381938..52386991,6	K562	blood:
5	chr10:52152378..52155454-chr10:52174313..52178963,4	MCF-7	breast:
6	chr10:52152624..52157680-chr10:52173844..52179255,6	K562	blood:

Variant related genes	Relation type
SGMS1	TF binding region
ENSG00000198964	Chromatin interaction
ENSG00000269700	Chromatin interaction
ENSG00000225303	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11006194	0.84[CHB][hapmap]
rs1203375	0.82[CEU][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs1203377	0.96[EUR][1000 genomes]
rs1203382	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs1203386	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1203390	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1203393	0.93[ASN][1000 genomes]
rs1203394	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203395	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203401	0.93[ASN][1000 genomes]
rs1203403	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203405	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203407	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203409	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203410	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203411	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203413	0.95[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1203415	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs1203420	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1740761	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs1810576	0.90[ASN][1000 genomes]
rs1916566	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs1916567	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2099527	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs2117958	0.93[EUR][1000 genomes]
rs2221	0.80[CEU][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs2339402	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2574985	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2688878	0.88[EUR][1000 genomes]
rs2842103	0.91[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs2842108	0.83[EUR][1000 genomes]
rs2842111	0.92[EUR][1000 genomes]
rs2983347	0.90[ASN][1000 genomes]
rs2983350	0.91[JPT][hapmap]
rs2983354	0.81[CEU][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2983357	0.84[JPT][hapmap];1.00[MEX][hapmap];0.80[ASN][1000 genomes]
rs2983359	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs2983361	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs2983368	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2983369	0.91[ASN][1000 genomes]
rs2983370	0.81[ASN][1000 genomes]
rs2983371	0.91[ASN][1000 genomes]
rs3011770	0.84[MEX][hapmap]
rs3011771	0.91[ASN][1000 genomes]
rs3011773	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.90[ASN][1000 genomes]
rs3011779	0.85[ASN][1000 genomes]
rs3011780	0.85[ASN][1000 genomes]
rs3011782	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs3011783	0.83[ASN][1000 genomes]
rs3011787	0.80[CEU][hapmap];0.91[ASN][1000 genomes]
rs3011788	0.80[CEU][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs3011789	0.80[ASN][1000 genomes]
rs3011790	0.84[JPT][hapmap];1.00[MEX][hapmap]
rs3011791	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs3011792	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs3011793	0.80[ASN][1000 genomes]
rs3011794	0.84[JPT][hapmap];1.00[MEX][hapmap];0.80[ASN][1000 genomes]
rs3011797	0.84[JPT][hapmap]
rs3011801	0.84[JPT][hapmap]
rs4312019	0.95[CEU][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs4536155	0.96[EUR][1000 genomes]
rs7092014	0.93[EUR][1000 genomes]
rs715675	0.96[EUR][1000 genomes]
rs7912351	0.84[ASN][1000 genomes]
rs920136	0.86[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes];0.95[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1203418	MSMB	cis	parietal	SCAN
rs1203418	PARG	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52176200-52178800	Active TSS	Right Atrium	heart
2	chr10:52176200-52178800	Active TSS	NHDF-Ad	bronchial
3	chr10:52176400-52178800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr10:52176400-52178800	Active TSS	HSMMtube	muscle
5	chr10:52176600-52178600	Active TSS	Fetal Muscle Trunk	muscle
6	chr10:52176600-52178800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr10:52176600-52178800	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr10:52176600-52178800	Active TSS	Colon Smooth Muscle	Colon
9	chr10:52176600-52178800	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr10:52176800-52178600	Active TSS	Aorta	Aorta
11	chr10:52176800-52178600	Active TSS	Left Ventricle	heart
12	chr10:52176800-52178600	Active TSS	Lung	lung
13	chr10:52176800-52178600	Active TSS	Right Ventricle	heart
14	chr10:52176800-52178800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr10:52176800-52179000	Active TSS	Stomach Smooth Muscle	stomach
16	chr10:52177000-52178600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:52177000-52178600	Active TSS	Brain Substantia Nigra	brain
18	chr10:52177000-52178800	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr10:52177000-52178800	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr10:52177000-52179000	Active TSS	A549	lung
21	chr10:52177200-52178600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr10:52177200-52178600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr10:52177200-52178600	Active TSS	Psoas Muscle	Psoas
24	chr10:52177400-52178600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr10:52177400-52178600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr10:52177400-52178800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr10:52177400-52178800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr10:52177600-52178600	Active TSS	H9 Cell Line	embryonic stem cell
29	chr10:52177600-52178800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr10:52177800-52178600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr10:52177800-52178600	Active TSS	Fetal Intestine Small	intestine
32	chr10:52177800-52178600	Active TSS	Rectal Smooth Muscle	rectum
33	chr10:52177800-52178600	Active TSS	HepG2	liver
34	chr10:52178200-52178600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr10:52178200-52178600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr10:52178200-52178600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
37	chr10:52178200-52178600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr10:52178200-52178600	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr10:52178200-52178600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr10:52178200-52178600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr10:52178200-52178600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr10:52178200-52178600	Flanking Active TSS	Fetal Brain Male	brain
43	chr10:52178200-52178600	Active TSS	Thymus	Thymus
44	chr10:52178200-52178600	Enhancers	Spleen	Spleen
45	chr10:52178200-52178800	Flanking Active TSS	NH-A	brain
46	chr10:52178200-52179000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr10:52178400-52178600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr10:52178400-52178600	Active TSS	H1 Cell Line	embryonic stem cell
49	chr10:52178400-52178600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr10:52178400-52178600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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