Variant report

Variant	rs176879
Chromosome Location	chr10:38401284-38401285
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1138252	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1329786	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176877	0.80[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2008449	0.98[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];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023299	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2023351	0.80[ASN][1000 genomes]
rs2144859	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2178962	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263162	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263163	0.81[ASN][1000 genomes]
rs2263164	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2384731	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[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];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2472178	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2472179	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2472181	0.81[ASN][1000 genomes]
rs2474554	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2474563	0.80[ASN][1000 genomes]
rs2474564	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[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];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2474571	0.81[ASN][1000 genomes]
rs2474572	0.96[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];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[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	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2474591	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474596	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474597	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474610	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2504120	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504121	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504127	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504139	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504140	0.81[ASN][1000 genomes]
rs2504141	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]
rs2504148	0.81[ASN][1000 genomes]
rs2505179	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505185	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[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	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505236	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505244	0.94[ASN][1000 genomes]
rs2505249	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505250	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2505251	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505252	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505258	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505259	0.90[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];0.90[AMR][1000 genomes];0.90[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];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9299760	0.80[ASN][1000 genomes]
rs932538	0.94[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs176879	HSD17B7P2	cis	Esophagus Mucosa	GTEx
rs176879	HSD17B7P2	cis	parietal	SCAN
rs176879	ZNF37A	cis	lymphoblastoid	seeQTL
rs176879	ZNF25	cis	cerebellum	SCAN
rs176879	HSD17B7P2	cis	Whole Blood	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38393600-38402400	Weak transcription	HSMMtube	muscle
2	chr10:38395200-38402400	Weak transcription	NHDF-Ad	bronchial
3	chr10:38395600-38401800	Weak transcription	Gastric	stomach
4	chr10:38395600-38401800	Weak transcription	Pancreas	Pancrea
5	chr10:38395600-38402200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:38395600-38402200	Weak transcription	HepG2	liver
7	chr10:38395600-38402400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr10:38395600-38402400	Weak transcription	NHEK	skin
9	chr10:38395600-38403600	Weak transcription	Osteobl	bone
10	chr10:38395800-38402200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr10:38396000-38401800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr10:38396000-38402200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr10:38396000-38402600	Weak transcription	HSMM	muscle
14	chr10:38396200-38402200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr10:38400600-38401400	ZNF genes & repeats	Liver	Liver
16	chr10:38400600-38401400	ZNF genes & repeats	Right Ventricle	heart
17	chr10:38400600-38401800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr10:38400600-38407400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
19	chr10:38400600-38416600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
20	chr10:38400800-38407600	ZNF genes & repeats	Ovary	ovary
21	chr10:38400800-38415000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr10:38401000-38401400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
23	chr10:38401000-38401400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
24	chr10:38401000-38401400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr10:38401000-38401400	Enhancers	Fetal Heart	heart
26	chr10:38401000-38411200	ZNF genes & repeats	Dnd41	blood
27	chr10:38401000-38411400	ZNF genes & repeats	Brain Hippocampus Middle	brain
28	chr10:38401200-38401400	ZNF genes & repeats	Primary T cells from cord blood	blood
29	chr10:38401200-38401400	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
30	chr10:38401200-38401400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr10:38401200-38401400	ZNF genes & repeats	Fetal Brain Female	brain
32	chr10:38401200-38411200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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