Variant report

Variant	rs626519
Chromosome Location	chr10:38311777-38311778
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154945807..154946769-chr10:38311737..38312282,2	Hela-S3	cervix:
2	chr10:38309471..38312276-chr10:38318881..38321681,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10764147	0.81[EUR][1000 genomes]
rs10827835	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10827836	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11011407	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1208559	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1208592	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][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];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1735577	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][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	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs200937	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs200939	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs200943	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2021650	0.85[CEU][hapmap]
rs2144849	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2180408	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2257186	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[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	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2504141	0.85[CEU][hapmap];0.86[CHD][hapmap]
rs2504155	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505202	0.81[CEU][hapmap];0.81[CHD][hapmap]
rs2505203	0.81[CEU][hapmap]
rs2505232	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2749592	0.82[JPT][hapmap]
rs3851078	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4934916	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs496627	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]
rs527163	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs619739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623149	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623454	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs639479	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640774	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs662945	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7069702	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7099777	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs719569	0.83[AMR][1000 genomes];0.86[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs626519	ZNF25	cis	cerebellum	SCAN
rs626519	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs626519	HSD17B7P2	cis	parietal	SCAN
rs626519	CUL2	cis	parietal	SCAN
rs626519	ZNF25	cis	parietal	SCAN
rs626519	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38300400-38319600	Weak transcription	Gastric	stomach
2	chr10:38300600-38318000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:38300600-38331600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:38300600-38336000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr10:38300600-38339400	Weak transcription	Psoas Muscle	Psoas
6	chr10:38300800-38322000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr10:38300800-38339200	Weak transcription	HSMMtube	muscle
8	chr10:38301200-38320400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr10:38301200-38325000	Weak transcription	NHLF	lung
10	chr10:38301400-38314200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr10:38301400-38316600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr10:38301400-38318800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr10:38301600-38312800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr10:38301600-38320000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr10:38301800-38326600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr10:38301800-38344400	Weak transcription	Hela-S3	cervix
17	chr10:38302000-38313000	Strong transcription	Brain Germinal Matrix	brain
18	chr10:38302400-38312200	Strong transcription	Fetal Thymus	thymus
19	chr10:38302400-38327400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr10:38302600-38314400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr10:38302800-38316800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr10:38302800-38327200	Strong transcription	Fetal Intestine Large	intestine
23	chr10:38302800-38327400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr10:38303000-38313000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr10:38303000-38313200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr10:38303000-38316600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr10:38303200-38312800	Strong transcription	Placenta	Placenta
28	chr10:38303200-38313200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr10:38303200-38320200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:38303200-38326400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr10:38303200-38327800	Strong transcription	Primary B cells from cord blood	blood
32	chr10:38303400-38316800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr10:38303800-38318200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr10:38304200-38326400	Strong transcription	Primary T cells from cord blood	blood
35	chr10:38304600-38312200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr10:38304600-38314200	Weak transcription	Esophagus	oesophagus
37	chr10:38304800-38313200	Strong transcription	Fetal Lung	lung
38	chr10:38305000-38325600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr10:38305400-38313000	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr10:38305600-38319800	Strong transcription	Liver	Liver
41	chr10:38307400-38314200	Weak transcription	Pancreas	Pancrea
42	chr10:38307400-38314400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr10:38307400-38316400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr10:38307400-38321400	Weak transcription	Lung	lung
45	chr10:38307400-38321400	Weak transcription	Spleen	Spleen
46	chr10:38307400-38321600	Weak transcription	Right Ventricle	heart
47	chr10:38307600-38314400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr10:38307600-38314400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr10:38307600-38315600	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr10:38307600-38316000	Weak transcription	Fetal Intestine Small	intestine

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