Variant report

Variant	rs1203413
Chromosome Location	chr10:52171498-52171499
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52163174..52165033-chr10:52169624..52171788,2	K562	blood:
2	chr10:52169351..52171614-chr10:52383137..52385648,2	K562	blood:
3	chr10:52169460..52174968-chr10:52176430..52182227,8	K562	blood:

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1011881	0.81[JPT][hapmap]
rs10740714	0.88[ASN][1000 genomes]
rs10763354	0.86[CHD][hapmap]
rs10763366	0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs10763529	0.81[JPT][hapmap]
rs10826100	0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs10826118	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10826126	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11005937	0.88[ASN][1000 genomes]
rs1203377	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1203382	0.85[TSI][hapmap]
rs1203386	0.85[TSI][hapmap]
rs1203410	0.85[TSI][hapmap]
rs1203415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203418	0.95[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1203420	0.97[EUR][1000 genomes]
rs1203421	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs1436206	0.81[LWK][hapmap];0.86[YRI][hapmap]
rs1436211	0.86[CHD][hapmap]
rs1569962	0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1569963	0.88[ASN][1000 genomes]
rs1740761	0.80[CEU][hapmap]
rs1916566	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1916567	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs2092996	0.81[JPT][hapmap]
rs2099527	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2117958	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144862	0.81[JPT][hapmap]
rs2339402	0.96[EUR][1000 genomes]
rs2339505	0.81[JPT][hapmap]
rs2574959	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2574985	0.90[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs2688878	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2842103	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842108	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2842111	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4312019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4536155	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4935712	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4935727	0.81[JPT][hapmap]
rs7071603	0.81[JPT][hapmap]
rs7075289	0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7092014	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs715675	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7904833	0.84[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs920136	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs978588	0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[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	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
7	nsv948006	chr10:52127164-52177684	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1203413	MSMB	cis	parietal	SCAN
rs1203413	PARG	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52147000-52176600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr10:52157200-52177600	Weak transcription	Spleen	Spleen
3	chr10:52157800-52172000	Weak transcription	Fetal Lung	lung
4	chr10:52157800-52173200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr10:52157800-52175400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr10:52157800-52176800	Weak transcription	Lung	lung
7	chr10:52158800-52172200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr10:52160800-52176800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr10:52163600-52176800	Weak transcription	Thymus	Thymus
10	chr10:52164400-52172400	Weak transcription	Ovary	ovary
11	chr10:52164400-52173800	Weak transcription	Psoas Muscle	Psoas
12	chr10:52164400-52174000	Weak transcription	Brain Angular Gyrus	brain
13	chr10:52164400-52177600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr10:52164600-52176600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr10:52165200-52171600	Weak transcription	Brain Anterior Caudate	brain
16	chr10:52165400-52171800	Weak transcription	Liver	Liver
17	chr10:52166600-52175800	Weak transcription	Primary T cells from cord blood	blood
18	chr10:52166600-52177400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr10:52166800-52177200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr10:52166800-52177400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr10:52167000-52176800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr10:52167000-52176800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr10:52167000-52177200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr10:52167000-52177400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr10:52167600-52173000	Weak transcription	HepG2	liver
26	chr10:52167600-52176800	Weak transcription	Primary B cells from cord blood	blood
27	chr10:52168000-52177400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr10:52168200-52171800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr10:52168600-52176200	Weak transcription	Right Atrium	heart
30	chr10:52168600-52176600	Weak transcription	Fetal Brain Male	brain
31	chr10:52169000-52172400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr10:52169200-52171600	Enhancers	Osteobl	bone
33	chr10:52169600-52171800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr10:52169600-52172200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr10:52169800-52172200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr10:52170000-52172000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr10:52170000-52172200	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr10:52170000-52174200	Enhancers	Brain Substantia Nigra	brain
39	chr10:52170200-52171600	Weak transcription	Stomach Mucosa	stomach
40	chr10:52170200-52171800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr10:52170200-52172200	Weak transcription	A549	lung
42	chr10:52170200-52176400	Weak transcription	Small Intestine	intestine
43	chr10:52170200-52176800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr10:52170400-52171600	Weak transcription	Adipose Nuclei	Adipose
45	chr10:52170400-52171600	Weak transcription	Fetal Intestine Large	intestine
46	chr10:52170400-52171600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr10:52170400-52175000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:52170400-52175000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr10:52170400-52175200	Enhancers	Hela-S3	cervix
50	chr10:52170400-52176200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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