Variant report

Variant	rs2504141
Chromosome Location	chr10:38386691-38386692
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1138252	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1329786	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13503	0.81[CEU][hapmap];0.86[CHD][hapmap]
rs1548255	0.94[ASW][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap]
rs176838	0.91[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap]
rs176876	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176877	0.80[ASN][1000 genomes]
rs176879	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176880	0.94[ASW][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap]
rs176882	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs176885	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176886	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs176887	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs176889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2008449	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2021649	0.81[ASN][1000 genomes]
rs2021650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023299	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2023351	0.80[ASN][1000 genomes]
rs2144859	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2178962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263162	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263163	0.81[ASN][1000 genomes]
rs2263164	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2384731	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2472150	0.85[CEU][hapmap];0.88[CHD][hapmap]
rs2472173	0.80[ASN][1000 genomes]
rs2472174	0.80[ASN][1000 genomes]
rs2472175	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2472176	0.81[ASN][1000 genomes]
rs2472177	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2472178	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2472179	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2472181	0.81[ASN][1000 genomes]
rs2474554	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2474563	0.80[ASN][1000 genomes]
rs2474564	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2474565	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2474566	0.81[ASN][1000 genomes]
rs2474567	0.81[ASN][1000 genomes]
rs2474568	0.94[ASW][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2474569	0.81[ASN][1000 genomes]
rs2474570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2474571	0.81[ASN][1000 genomes]
rs2474572	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2474573	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474574	0.81[ASN][1000 genomes]
rs2474575	0.81[ASN][1000 genomes]
rs2474579	0.81[ASN][1000 genomes]
rs2474580	0.81[ASN][1000 genomes]
rs2474581	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2474591	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474596	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474597	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474610	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2504120	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504121	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504127	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504140	0.81[ASN][1000 genomes]
rs2504148	0.81[ASN][1000 genomes]
rs2505179	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505185	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505186	0.81[ASN][1000 genomes]
rs2505187	0.81[ASN][1000 genomes]
rs2505188	0.81[ASN][1000 genomes]
rs2505190	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505191	0.81[ASN][1000 genomes]
rs2505192	0.82[JPT][hapmap]
rs2505193	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2505194	0.94[ASW][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2505195	0.80[ASN][1000 genomes]
rs2505196	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2505197	0.81[ASN][1000 genomes]
rs2505198	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2505202	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs2505203	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2505232	0.83[CEU][hapmap]
rs2505235	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505236	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505244	0.94[ASN][1000 genomes]
rs2505249	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505250	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2505251	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505252	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505258	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505259	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2800485	0.94[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap]
rs2983343	0.81[ASN][1000 genomes]
rs496627	0.85[CEU][hapmap];0.86[CHD][hapmap]
rs619739	0.84[CEU][hapmap]
rs626519	0.85[CEU][hapmap];0.86[CHD][hapmap]
rs629577	0.85[CEU][hapmap]
rs645064	0.85[CEU][hapmap];0.88[CHD][hapmap]
rs6482060	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7915062	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9299760	0.80[ASN][1000 genomes]
rs932538	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9418322	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv540566	chr10:38301001-38680127	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv550419	chr10:38311777-38501654	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv6465	chr10:38377662-38422125	Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2504141	HSD17B7P2	cis	Whole Blood	GTEx
rs2504141	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs2504141	ZNF37A	cis	lymphoblastoid	seeQTL
rs2504141	HSD17B7P2	cis	parietal	SCAN
rs2504141	HSD17B7P2	cis	Esophagus Mucosa	GTEx
rs2504141	ZNF37A	cis	parietal	SCAN
rs2504141	ZNF25	cis	cerebellum	SCAN
rs2504141	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38384000-38388400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:38384200-38389000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr10:38384200-38389200	Weak transcription	Aorta	Aorta
4	chr10:38384400-38386800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr10:38384400-38388200	Weak transcription	Psoas Muscle	Psoas
6	chr10:38384400-38388800	Weak transcription	Fetal Intestine Small	intestine
7	chr10:38384400-38389200	Weak transcription	Small Intestine	intestine
8	chr10:38384400-38389400	Weak transcription	Thymus	Thymus
9	chr10:38384400-38396400	Weak transcription	HUVEC	blood vessel
10	chr10:38384600-38386800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr10:38384600-38386800	Strong transcription	Fetal Lung	lung
12	chr10:38384600-38387800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr10:38384600-38388000	Strong transcription	Placenta	Placenta
14	chr10:38384600-38388000	Weak transcription	NHLF	lung
15	chr10:38384600-38388200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr10:38384600-38388200	Strong transcription	Fetal Muscle Leg	muscle
17	chr10:38384600-38388600	Strong transcription	Fetal Muscle Trunk	muscle
18	chr10:38384600-38388600	ZNF genes & repeats	A549	lung
19	chr10:38384600-38388600	Strong transcription	NH-A	brain
20	chr10:38384600-38388800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr10:38384600-38389200	Weak transcription	Esophagus	oesophagus
22	chr10:38384600-38390600	Weak transcription	Fetal Heart	heart
23	chr10:38384600-38390800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr10:38384600-38390800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr10:38384600-38391200	Weak transcription	Colonic Mucosa	Colon
26	chr10:38384600-38391400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr10:38384600-38391400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr10:38384600-38391400	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr10:38384600-38391800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:38384600-38392800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr10:38384600-38392800	Weak transcription	Gastric	stomach
32	chr10:38384800-38386800	Weak transcription	Brain Angular Gyrus	brain
33	chr10:38384800-38387000	Strong transcription	Fetal Intestine Large	intestine
34	chr10:38384800-38387200	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr10:38384800-38387400	Strong transcription	HMEC	breast
36	chr10:38384800-38387600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr10:38384800-38387600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr10:38384800-38387800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr10:38384800-38387800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr10:38384800-38387800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr10:38384800-38387800	Strong transcription	Osteobl	bone
42	chr10:38384800-38388200	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr10:38384800-38388200	Strong transcription	Stomach Smooth Muscle	stomach
44	chr10:38384800-38388400	Strong transcription	Brain Hippocampus Middle	brain
45	chr10:38384800-38388600	Strong transcription	Brain Substantia Nigra	brain
46	chr10:38384800-38388600	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr10:38384800-38388600	ZNF genes & repeats	GM12878-XiMat	blood
48	chr10:38384800-38388600	Strong transcription	K562	blood
49	chr10:38384800-38388600	Strong transcription	NHDF-Ad	bronchial
50	chr10:38384800-38389000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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