Variant report

Variant	rs13503
Chromosome Location	chr10:38239843-38239844
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1022698	0.80[AMR][1000 genomes]
rs10764147	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10827835	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10827836	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11011407	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1208559	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1208592	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1208681	0.83[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1208684	0.83[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1208689	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1208767	0.80[AMR][1000 genomes]
rs1735577	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs176879	0.81[CEU][hapmap];0.86[CHD][hapmap]
rs176885	0.81[CEU][hapmap];0.86[CHD][hapmap]
rs176889	0.81[CEU][hapmap]
rs1779017	0.80[AMR][1000 genomes]
rs200903	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs200910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs200924	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs200935	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs200936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs200937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs200939	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs200943	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2021650	0.81[CEU][hapmap]
rs2144849	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2180408	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2257186	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2472150	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2472177	0.86[CHD][hapmap];0.84[GIH][hapmap]
rs2474570	0.81[CEU][hapmap];0.86[CHD][hapmap]
rs2474573	0.81[CEU][hapmap];0.86[CHD][hapmap]
rs2504130	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2504141	0.81[CEU][hapmap];0.86[CHD][hapmap]
rs2504155	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2505232	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2749592	0.82[JPT][hapmap]
rs3851078	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4934916	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs496627	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs527163	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs619739	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs623149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs623454	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs626519	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs629577	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs639479	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs640774	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs645064	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs662945	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7069702	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7099777	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs719569	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7915062	0.81[CEU][hapmap];0.86[CHD][hapmap]

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	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1051121	chr10:38155991-38426204	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv540565	chr10:38155991-38426204	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv1052703	chr10:38174640-38266472	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13503	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs13503	ZNF25	cis	parietal	SCAN
rs13503	HSD17B7P2	cis	parietal	SCAN
rs13503	ZNF25	cis	cerebellum	SCAN
rs13503	CUL2	cis	parietal	SCAN
rs13503	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38201400-38240000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr10:38220800-38241000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr10:38223400-38241000	Weak transcription	Brain Angular Gyrus	brain
4	chr10:38223600-38240600	Weak transcription	Aorta	Aorta
5	chr10:38227400-38241000	Weak transcription	Colon Smooth Muscle	Colon
6	chr10:38227400-38241600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr10:38229400-38241000	Weak transcription	Fetal Brain Male	brain
8	chr10:38229600-38240600	Weak transcription	Right Ventricle	heart
9	chr10:38232000-38240200	Weak transcription	Fetal Brain Female	brain
10	chr10:38232400-38241000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:38232600-38240400	Weak transcription	Fetal Lung	lung
12	chr10:38233000-38240000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr10:38233000-38241200	Weak transcription	Esophagus	oesophagus
14	chr10:38233200-38240400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr10:38233400-38240200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr10:38233400-38241000	Weak transcription	Spleen	Spleen
17	chr10:38234000-38241600	Weak transcription	Small Intestine	intestine
18	chr10:38234200-38241000	Weak transcription	Thymus	Thymus
19	chr10:38234800-38240200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr10:38234800-38241000	Weak transcription	Brain Germinal Matrix	brain
21	chr10:38235000-38240800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr10:38236000-38241000	Weak transcription	A549	lung
23	chr10:38236400-38240200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr10:38236400-38241000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr10:38236400-38243800	Weak transcription	Fetal Stomach	stomach
26	chr10:38236800-38241000	Weak transcription	Gastric	stomach
27	chr10:38236800-38241200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr10:38236800-38241400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr10:38236800-38241600	Strong transcription	Stomach Smooth Muscle	stomach
30	chr10:38236800-38249000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr10:38237200-38240200	Weak transcription	Primary T cells from cord blood	blood
32	chr10:38237200-38241000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr10:38237200-38241000	Weak transcription	Osteobl	bone
34	chr10:38237400-38240600	Weak transcription	HSMM	muscle
35	chr10:38237400-38241000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr10:38237600-38240200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr10:38237600-38240800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr10:38237800-38241200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr10:38237800-38247200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr10:38238000-38240600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr10:38238000-38240600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr10:38238000-38244200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr10:38238000-38248600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr10:38238200-38240400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr10:38238200-38240600	Weak transcription	NHDF-Ad	bronchial
46	chr10:38238200-38240800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr10:38238200-38241000	Weak transcription	Fetal Intestine Large	intestine
48	chr10:38238200-38241000	Weak transcription	Pancreas	Pancrea
49	chr10:38238400-38240800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr10:38238400-38240800	Weak transcription	Primary B cells from cord blood	blood

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