Variant report

Variant	rs176885
Chromosome Location	chr10:38402789-38402790
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:38402369..38404605-chr10:38405748..38407768,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1138252	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329786	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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];0.99[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176880	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]
rs176882	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];0.81[ASN][1000 genomes]
rs176887	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
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];1.00[ASN][1000 genomes]
rs1813028	0.81[ASN][1000 genomes]
rs2008449	0.98[AFR][1000 genomes];0.97[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];0.99[ASN][1000 genomes]
rs2023299	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2144859	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2178962	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2263162	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2263164	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2384731	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2472150	0.85[CEU][hapmap];0.88[CHD][hapmap]
rs2472175	0.91[CHB][hapmap];0.91[JPT][hapmap]
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];0.99[ASN][1000 genomes]
rs2472178	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2472179	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2474554	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2474564	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2474565	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2474568	0.94[ASW][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap]
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];0.93[ASN][1000 genomes]
rs2474572	0.96[AFR][1000 genomes];0.99[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];0.99[ASN][1000 genomes]
rs2474581	0.98[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2474591	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2474596	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2474597	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2474610	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2504120	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504121	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504127	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504139	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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];0.99[ASN][1000 genomes]
rs2505179	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505185	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505190	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505192	0.82[JPT][hapmap]
rs2505193	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2505194	0.94[ASW][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap]
rs2505196	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2505198	0.94[AFR][1000 genomes];0.96[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];0.97[ASN][1000 genomes]
rs2505236	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505244	0.96[ASN][1000 genomes]
rs2505249	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505250	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505251	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505252	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505258	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505259	0.90[AFR][1000 genomes];0.96[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]
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];0.96[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];0.97[ASN][1000 genomes]
rs932538	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	nsv895031	chr10:38402789-38464886	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs176885	ZNF25	cis	cerebellum	SCAN
rs176885	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs176885	HSD17B7P2	cis	Whole Blood	GTEx
rs176885	ZNF37A	cis	lymphoblastoid	seeQTL
rs176885	LOC399744	cis	parietal	SCAN
rs176885	HSD17B7P2	cis	Esophagus Mucosa	GTEx
rs176885	HSD17B7P2	cis	parietal	SCAN
rs176885	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	chr10:38395600-38403600	Weak transcription	Osteobl	bone
2	chr10:38400600-38407400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
3	chr10:38400600-38416600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr10:38400800-38407600	ZNF genes & repeats	Ovary	ovary
5	chr10:38400800-38415000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr10:38401000-38411200	ZNF genes & repeats	Dnd41	blood
7	chr10:38401000-38411400	ZNF genes & repeats	Brain Hippocampus Middle	brain
8	chr10:38401200-38411200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr10:38401400-38404200	Weak transcription	Fetal Heart	heart
10	chr10:38401600-38402800	ZNF genes & repeats	Fetal Stomach	stomach
11	chr10:38401800-38402800	ZNF genes & repeats	Aorta	Aorta
12	chr10:38401800-38402800	ZNF genes & repeats	Gastric	stomach
13	chr10:38401800-38402800	ZNF genes & repeats	Pancreas	Pancrea
14	chr10:38401800-38407600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr10:38401800-38407600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
16	chr10:38401800-38407800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
17	chr10:38401800-38407800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
18	chr10:38401800-38408200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
19	chr10:38401800-38411200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr10:38401800-38413800	ZNF genes & repeats	Adipose Nuclei	Adipose
21	chr10:38402000-38406200	ZNF genes & repeats	Spleen	Spleen
22	chr10:38402000-38407400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
23	chr10:38402000-38408000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
24	chr10:38402000-38409200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
25	chr10:38402000-38412800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
26	chr10:38402200-38402800	ZNF genes & repeats	Psoas Muscle	Psoas
27	chr10:38402200-38402800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
28	chr10:38402200-38403400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr10:38402200-38403800	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
30	chr10:38402200-38404600	Strong transcription	HepG2	liver
31	chr10:38402200-38406400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
32	chr10:38402200-38406800	ZNF genes & repeats	Thymus	Thymus
33	chr10:38402200-38407200	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr10:38402200-38407600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
35	chr10:38402200-38407600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
36	chr10:38402200-38407600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
37	chr10:38402200-38407600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
38	chr10:38402200-38408000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
39	chr10:38402200-38408000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr10:38402200-38408200	ZNF genes & repeats	Fetal Lung	lung
41	chr10:38402200-38408200	ZNF genes & repeats	Left Ventricle	heart
42	chr10:38402200-38408400	ZNF genes & repeats	Primary B cells from cord blood	blood
43	chr10:38402200-38408400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr10:38402200-38408400	ZNF genes & repeats	Brain Angular Gyrus	brain
45	chr10:38402200-38408400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
46	chr10:38402200-38408800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr10:38402200-38408800	ZNF genes & repeats	Brain Cingulate Gyrus	brain
48	chr10:38402200-38409000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
49	chr10:38402200-38409200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr10:38402200-38409200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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