Variant report

Variant	rs496627
Chromosome Location	chr10:38350398-38350399
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10764147	0.82[AMR][1000 genomes]
rs10827835	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10827836	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11011407	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1208592	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13503	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1735577	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs176879	0.85[CEU][hapmap];0.86[CHD][hapmap]
rs176885	0.85[CEU][hapmap];0.86[CHD][hapmap]
rs176889	0.85[CEU][hapmap]
rs200936	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs200937	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs200939	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs200943	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2021650	0.85[CEU][hapmap]
rs2144849	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2180408	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2257186	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2472150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2472177	0.86[CHD][hapmap];0.84[GIH][hapmap]
rs2474570	0.84[CEU][hapmap];0.86[CHD][hapmap]
rs2474573	0.85[CEU][hapmap];0.86[CHD][hapmap]
rs2504130	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2504141	0.85[CEU][hapmap];0.86[CHD][hapmap]
rs2504155	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505202	0.81[CEU][hapmap];0.81[CHD][hapmap]
rs2505203	0.81[CEU][hapmap]
rs2505232	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2749592	0.82[JPT][hapmap]
rs2800485	0.81[CHD][hapmap];0.87[GIH][hapmap]
rs3851078	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4934916	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs527163	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs619739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs623149	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs623454	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs626519	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];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs629577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs639479	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs640774	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs645064	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs662945	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7069702	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7099777	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs719569	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7915062	0.85[CEU][hapmap];0.86[CHD][hapmap]

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	nsv534122	chr10:38240258-38356008	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	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
9	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs496627	ZNF25	cis	parietal	SCAN
rs496627	CUL2	cis	parietal	SCAN
rs496627	HSD17B7P2	cis	parietal	SCAN
rs496627	ZNF25	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38334000-38350600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
2	chr10:38336200-38351600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:38340800-38351200	ZNF genes & repeats	Liver	Liver
4	chr10:38340800-38351600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
5	chr10:38340800-38353400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
6	chr10:38341200-38351200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
7	chr10:38341200-38353800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr10:38341600-38351200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
9	chr10:38341600-38351400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr10:38341600-38351600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr10:38342000-38351200	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr10:38342200-38350400	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
13	chr10:38345200-38350600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr10:38345400-38355200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr10:38345600-38350400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr10:38345600-38353400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr10:38345600-38354400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr10:38345800-38353200	Strong transcription	Dnd41	blood
19	chr10:38346000-38351400	Strong transcription	Stomach Smooth Muscle	stomach
20	chr10:38346000-38353200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr10:38346200-38350600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr10:38346200-38351200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr10:38346200-38358200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr10:38346400-38350600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr10:38346800-38351000	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr10:38346800-38352400	Weak transcription	Hela-S3	cervix
27	chr10:38346800-38352600	Weak transcription	Fetal Thymus	thymus
28	chr10:38347000-38351200	Weak transcription	Stomach Mucosa	stomach
29	chr10:38347000-38351600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr10:38347000-38351600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr10:38347000-38358200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr10:38347200-38352000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr10:38347800-38351600	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr10:38347800-38351600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr10:38347800-38351800	Weak transcription	HSMMtube	muscle
36	chr10:38348000-38351000	Strong transcription	Fetal Lung	lung
37	chr10:38348000-38351200	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr10:38348000-38351400	Strong transcription	Fetal Kidney	kidney
39	chr10:38348200-38352000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr10:38348200-38353400	Strong transcription	Primary B cells from cord blood	blood
41	chr10:38348600-38350600	Strong transcription	Ovary	ovary
42	chr10:38348600-38351200	Strong transcription	Rectal Smooth Muscle	rectum
43	chr10:38348800-38351600	Strong transcription	Brain Hippocampus Middle	brain
44	chr10:38348800-38354800	Strong transcription	Primary T cells from cord blood	blood
45	chr10:38349000-38350400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr10:38349000-38351200	Strong transcription	Fetal Muscle Leg	muscle
47	chr10:38349200-38350400	Strong transcription	Brain Angular Gyrus	brain
48	chr10:38349200-38350400	Strong transcription	Right Ventricle	heart
49	chr10:38349200-38350400	Strong transcription	HepG2	liver
50	chr10:38349200-38350600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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