Variant report

Variant	rs2505196
Chromosome Location	chr10:38393563-38393564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs11011452	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11011461	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1548255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs176838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs176876	0.81[ASN][1000 genomes]
rs176877	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176879	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs176880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176881	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs176882	0.81[ASN][1000 genomes]
rs176885	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs176886	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176889	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs1813028	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1854563	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1985707	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1998062	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2008449	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2021649	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2021650	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2023299	0.80[ASN][1000 genomes]
rs2023351	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2178962	0.81[ASN][1000 genomes]
rs2180412	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2263162	0.81[ASN][1000 genomes]
rs2263163	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263164	0.81[ASN][1000 genomes]
rs2384730	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2472173	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2472174	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2472175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2472176	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2472177	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2472178	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2472180	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2472181	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2472183	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2474563	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2474565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2474566	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474567	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474569	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474570	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2474571	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474572	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2474573	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2474574	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474575	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474579	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474580	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474581	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2474584	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474586	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474587	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474588	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474590	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2474594	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474595	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474598	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2474599	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2504120	0.81[ASN][1000 genomes]
rs2504121	0.81[ASN][1000 genomes]
rs2504127	0.81[ASN][1000 genomes]
rs2504139	0.81[ASN][1000 genomes]
rs2504140	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504141	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2504142	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2504143	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504148	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504149	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505186	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505187	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505188	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505189	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505191	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505195	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505198	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2505202	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2505203	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs2505237	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505241	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2505248	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505259	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2505260	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2800485	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs2983343	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71491246	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7915062	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs9299760	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs932538	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9417297	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9418322	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2505196	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs2505196	ZNF37A	Cis_1M	lymphoblastoid	RTeQTL
rs2505196	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38384400-38396400	Weak transcription	HUVEC	blood vessel
2	chr10:38385400-38394400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:38385600-38396200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr10:38386000-38395200	Weak transcription	Hela-S3	cervix
5	chr10:38386200-38396000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr10:38386800-38395800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr10:38386800-38396200	ZNF genes & repeats	Fetal Brain Female	brain
8	chr10:38386800-38396200	ZNF genes & repeats	Fetal Lung	lung
9	chr10:38387600-38398800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr10:38387800-38396800	ZNF genes & repeats	Liver	Liver
11	chr10:38388200-38396200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr10:38388200-38399200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
13	chr10:38388600-38394800	Weak transcription	NHDF-Ad	bronchial
14	chr10:38388600-38397600	Weak transcription	NH-A	brain
15	chr10:38389200-38395800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
16	chr10:38389200-38396000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
17	chr10:38389600-38395800	ZNF genes & repeats	Dnd41	blood
18	chr10:38389800-38393800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
19	chr10:38390000-38395800	ZNF genes & repeats	Adipose Nuclei	Adipose
20	chr10:38390400-38393800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
21	chr10:38390600-38394000	ZNF genes & repeats	Fetal Intestine Large	intestine
22	chr10:38390600-38395600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
23	chr10:38390600-38396000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr10:38390800-38393800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr10:38390800-38395600	ZNF genes & repeats	Colon Smooth Muscle	Colon
26	chr10:38391000-38393800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
27	chr10:38391000-38393800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr10:38391000-38395600	ZNF genes & repeats	A549	lung
29	chr10:38391000-38396000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:38391000-38396200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr10:38391200-38393600	ZNF genes & repeats	Brain Anterior Caudate	brain
32	chr10:38391200-38393600	ZNF genes & repeats	Brain Substantia Nigra	brain
33	chr10:38391200-38393800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
34	chr10:38391200-38393800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
35	chr10:38391200-38395000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr10:38391200-38395600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
37	chr10:38391200-38395600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
38	chr10:38391200-38396000	ZNF genes & repeats	Fetal Kidney	kidney
39	chr10:38391200-38396400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
40	chr10:38391600-38393600	ZNF genes & repeats	GM12878-XiMat	blood
41	chr10:38391600-38395600	ZNF genes & repeats	Fetal Brain Male	brain
42	chr10:38391600-38395800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr10:38391600-38396000	ZNF genes & repeats	Primary B cells from cord blood	blood
44	chr10:38391800-38393800	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
45	chr10:38391800-38394600	Weak transcription	Osteobl	bone
46	chr10:38391800-38395600	ZNF genes & repeats	Primary T cells from cord blood	blood
47	chr10:38392000-38394800	Weak transcription	HepG2	liver
48	chr10:38392200-38395600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr10:38392200-38395600	ZNF genes & repeats	Fetal Muscle Leg	muscle
50	chr10:38392400-38395600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links