Variant report

Variant	rs200939
Chromosome Location	chr10:38139483-38139484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1022698	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10764147	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10827835	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10827836	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11011343	0.82[ASN][1000 genomes]
rs11011351	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11011407	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1208559	0.88[ASN][1000 genomes]
rs1208592	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1208681	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1208684	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1208689	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1208708	0.86[ASN][1000 genomes]
rs1208767	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12774732	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13503	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1735577	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1779017	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1814077	0.82[ASN][1000 genomes]
rs200903	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200910	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200924	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs200935	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200936	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs200937	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs200943	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2144849	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2180408	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2257186	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2472150	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2504130	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2504155	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2505232	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs289649	0.82[ASN][1000 genomes]
rs3851078	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4934906	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4934907	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4934912	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4934916	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs496627	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs527163	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs619739	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs623149	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs623454	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs626519	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs629577	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs639479	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs640774	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs645064	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs662945	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7069702	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7099777	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs719569	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9417256	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs200939	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs200939	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38123000-38144400	Weak transcription	NHEK	skin
2	chr10:38124000-38144400	Weak transcription	NH-A	brain
3	chr10:38125200-38144400	Weak transcription	Psoas Muscle	Psoas
4	chr10:38125600-38142800	Weak transcription	NHDF-Ad	bronchial
5	chr10:38125800-38143200	Weak transcription	HepG2	liver
6	chr10:38125800-38144400	Weak transcription	HMEC	breast
7	chr10:38126600-38145600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr10:38126800-38144800	Weak transcription	Thymus	Thymus
9	chr10:38127000-38142800	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:38127000-38143600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr10:38127000-38143600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr10:38127000-38143800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr10:38127000-38144200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr10:38127000-38144400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr10:38127000-38144400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr10:38127000-38144400	Weak transcription	HSMMtube	muscle
17	chr10:38127000-38144600	Weak transcription	K562	blood
18	chr10:38127000-38145200	Weak transcription	Gastric	stomach
19	chr10:38127000-38145600	Weak transcription	Colonic Mucosa	Colon
20	chr10:38127200-38143000	Weak transcription	Brain Hippocampus Middle	brain
21	chr10:38127200-38144400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr10:38127200-38144400	Weak transcription	Osteobl	bone
23	chr10:38127200-38145800	Weak transcription	Placenta	Placenta
24	chr10:38127400-38142800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr10:38127400-38143000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr10:38127400-38143600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr10:38127400-38144000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr10:38127400-38144000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr10:38127400-38144400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr10:38127400-38144400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr10:38127600-38143400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr10:38127600-38143400	Weak transcription	Brain Anterior Caudate	brain
33	chr10:38127600-38145200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:38127800-38143400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr10:38128000-38144400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr10:38128200-38143800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr10:38128200-38144400	Weak transcription	Left Ventricle	heart
38	chr10:38128400-38145000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr10:38128800-38143200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr10:38128800-38145400	Weak transcription	Primary B cells from cord blood	blood
41	chr10:38129400-38143600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr10:38129800-38142800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr10:38132000-38141200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr10:38132000-38144400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr10:38132000-38145200	Weak transcription	Aorta	Aorta
46	chr10:38132200-38142800	Weak transcription	Dnd41	blood
47	chr10:38132200-38144600	Weak transcription	Small Intestine	intestine
48	chr10:38132400-38145800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr10:38133200-38143200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr10:38133200-38144400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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