Variant report

Variant	rs2504139
Chromosome Location	chr10:38388321-38388322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

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]
rs176876	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176877	0.80[ASN][1000 genomes]
rs176879	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176882	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs176885	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176889	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[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]
rs2472173	0.80[ASN][1000 genomes]
rs2472174	0.80[ASN][1000 genomes]
rs2472175	0.81[ASN][1000 genomes]
rs2472176	0.81[ASN][1000 genomes]
rs2472177	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]
rs2474566	0.81[ASN][1000 genomes]
rs2474567	0.81[ASN][1000 genomes]
rs2474568	0.81[ASN][1000 genomes]
rs2474569	0.81[ASN][1000 genomes]
rs2474570	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	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]
rs2504140	0.81[ASN][1000 genomes]
rs2504141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
rs2505193	0.81[ASN][1000 genomes]
rs2505194	0.80[ASN][1000 genomes]
rs2505195	0.80[ASN][1000 genomes]
rs2505196	0.81[ASN][1000 genomes]
rs2505197	0.81[ASN][1000 genomes]
rs2505198	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
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]
rs2983343	0.81[ASN][1000 genomes]
rs6482060	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7915062	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2504139	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs2504139	HSD17B7P2	cis	Whole Blood	GTEx
rs2504139	HSD17B7P2	cis	Esophagus Mucosa	GTEx
rs2504139	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 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	chr10:38384400-38388800	Weak transcription	Fetal Intestine Small	intestine
5	chr10:38384400-38389200	Weak transcription	Small Intestine	intestine
6	chr10:38384400-38389400	Weak transcription	Thymus	Thymus
7	chr10:38384400-38396400	Weak transcription	HUVEC	blood vessel
8	chr10:38384600-38388600	Strong transcription	Fetal Muscle Trunk	muscle
9	chr10:38384600-38388600	ZNF genes & repeats	A549	lung
10	chr10:38384600-38388600	Strong transcription	NH-A	brain
11	chr10:38384600-38388800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr10:38384600-38389200	Weak transcription	Esophagus	oesophagus
13	chr10:38384600-38390600	Weak transcription	Fetal Heart	heart
14	chr10:38384600-38390800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr10:38384600-38390800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr10:38384600-38391200	Weak transcription	Colonic Mucosa	Colon
17	chr10:38384600-38391400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr10:38384600-38391400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr10:38384600-38391400	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr10:38384600-38391800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr10:38384600-38392800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr10:38384600-38392800	Weak transcription	Gastric	stomach
23	chr10:38384800-38388400	Strong transcription	Brain Hippocampus Middle	brain
24	chr10:38384800-38388600	Strong transcription	Brain Substantia Nigra	brain
25	chr10:38384800-38388600	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr10:38384800-38388600	ZNF genes & repeats	GM12878-XiMat	blood
27	chr10:38384800-38388600	Strong transcription	K562	blood
28	chr10:38384800-38388600	Strong transcription	NHDF-Ad	bronchial
29	chr10:38384800-38389000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr10:38384800-38389000	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr10:38384800-38389200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr10:38384800-38390200	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr10:38384800-38390600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr10:38384800-38390800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr10:38384800-38391000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:38384800-38391000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr10:38384800-38391600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr10:38384800-38392800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr10:38384800-38392800	Weak transcription	Spleen	Spleen
40	chr10:38385000-38388800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr10:38385000-38389800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr10:38385000-38392800	Weak transcription	Pancreas	Pancrea
43	chr10:38385200-38388400	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr10:38385200-38388400	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr10:38385200-38388400	Strong transcription	Fetal Brain Male	brain
46	chr10:38385200-38388600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr10:38385200-38388600	Strong transcription	HSMM	muscle
48	chr10:38385200-38388800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr10:38385200-38389200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr10:38385200-38389600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links