Variant report

Variant	rs176889
Chromosome Location	chr10:38407519-38407520
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: 4 )

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

rs_ID	r²[population]
rs1138252	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329786	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13503	0.81[CEU][hapmap]
rs1548255	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs176838	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs176876	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176879	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]
rs176880	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs176882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176885	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]
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]
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];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2023299	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2144859	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2178962	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2263162	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2263164	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2384731	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2472150	0.85[CEU][hapmap]
rs2472175	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2472177	1.00[CHB][hapmap];1.00[JPT][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];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2474564	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2474565	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2474568	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2474570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2474572	0.96[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2474573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[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];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2474596	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2474597	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2474610	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2504120	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504121	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504127	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504139	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504141	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]
rs2505179	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505185	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505190	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505192	0.82[JPT][hapmap]
rs2505193	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2505194	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2505196	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs2505198	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2505202	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs2505203	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2505232	0.84[CEU][hapmap]
rs2505235	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505236	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505250	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505251	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505252	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505258	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505259	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2800485	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs496627	0.85[CEU][hapmap]
rs619739	0.85[CEU][hapmap]
rs626519	0.85[CEU][hapmap]
rs629577	0.86[CEU][hapmap]
rs645064	0.85[CEU][hapmap]
rs6482060	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7915062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs176889	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs176889	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs176889	HSD17B7P2	cis	Whole Blood	GTEx
rs176889	HSD17B7P2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38400600-38416600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
2	chr10:38400800-38407600	ZNF genes & repeats	Ovary	ovary
3	chr10:38400800-38415000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr10:38401000-38411200	ZNF genes & repeats	Dnd41	blood
5	chr10:38401000-38411400	ZNF genes & repeats	Brain Hippocampus Middle	brain
6	chr10:38401200-38411200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr10:38401800-38407600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr10:38401800-38407600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
9	chr10:38401800-38407800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
10	chr10:38401800-38407800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
11	chr10:38401800-38408200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
12	chr10:38401800-38411200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr10:38401800-38413800	ZNF genes & repeats	Adipose Nuclei	Adipose
14	chr10:38402000-38408000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
15	chr10:38402000-38409200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr10:38402000-38412800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr10:38402200-38407600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
18	chr10:38402200-38407600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
19	chr10:38402200-38407600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
20	chr10:38402200-38407600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
21	chr10:38402200-38408000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr10:38402200-38408000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr10:38402200-38408200	ZNF genes & repeats	Fetal Lung	lung
24	chr10:38402200-38408200	ZNF genes & repeats	Left Ventricle	heart
25	chr10:38402200-38408400	ZNF genes & repeats	Primary B cells from cord blood	blood
26	chr10:38402200-38408400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr10:38402200-38408400	ZNF genes & repeats	Brain Angular Gyrus	brain
28	chr10:38402200-38408400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
29	chr10:38402200-38408800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr10:38402200-38408800	ZNF genes & repeats	Brain Cingulate Gyrus	brain
31	chr10:38402200-38409000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
32	chr10:38402200-38409200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr10:38402200-38409200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr10:38402200-38410000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
35	chr10:38402200-38411000	ZNF genes & repeats	Fetal Brain Female	brain
36	chr10:38402200-38411200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr10:38402200-38413200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
38	chr10:38402200-38413200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr10:38402200-38413400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr10:38402200-38413400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
41	chr10:38402200-38413600	ZNF genes & repeats	Liver	Liver
42	chr10:38402400-38407800	ZNF genes & repeats	GM12878-XiMat	blood
43	chr10:38402400-38408200	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
44	chr10:38402400-38408200	ZNF genes & repeats	Brain Germinal Matrix	brain
45	chr10:38402400-38408400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
46	chr10:38402400-38408400	ZNF genes & repeats	Brain Anterior Caudate	brain
47	chr10:38402400-38408400	ZNF genes & repeats	Fetal Muscle Leg	muscle
48	chr10:38402400-38408400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
49	chr10:38402400-38408400	ZNF genes & repeats	A549	lung
50	chr10:38402400-38408800	ZNF genes & repeats	HSMMtube	muscle

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