Variant report

Variant	rs662945
Chromosome Location	chr10:38322766-38322767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10764147	0.83[AMR][1000 genomes]
rs10827835	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10827836	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11011407	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1208592	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13503	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1735577	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs200910	0.83[AMR][1000 genomes]
rs200924	0.83[AMR][1000 genomes]
rs200935	0.83[AMR][1000 genomes]
rs200936	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs200937	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs200939	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs200943	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2144849	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2180408	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2257186	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2472150	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2504130	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2504155	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505232	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3851078	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4934916	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs496627	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs527163	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs619739	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs623149	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs623454	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs626519	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs629577	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs639479	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs640774	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs645064	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7069702	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7099777	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs719569	0.87[AMR][1000 genomes];0.85[EUR][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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs662945	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs662945	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38300600-38331600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:38300600-38336000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:38300600-38339400	Weak transcription	Psoas Muscle	Psoas
4	chr10:38300800-38339200	Weak transcription	HSMMtube	muscle
5	chr10:38301200-38325000	Weak transcription	NHLF	lung
6	chr10:38301800-38326600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr10:38301800-38344400	Weak transcription	Hela-S3	cervix
8	chr10:38302400-38327400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr10:38302800-38327200	Strong transcription	Fetal Intestine Large	intestine
10	chr10:38302800-38327400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:38303200-38326400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr10:38303200-38327800	Strong transcription	Primary B cells from cord blood	blood
13	chr10:38304200-38326400	Strong transcription	Primary T cells from cord blood	blood
14	chr10:38305000-38325600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr10:38307600-38346600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:38307800-38327600	Weak transcription	NHDF-Ad	bronchial
17	chr10:38307800-38336200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr10:38307800-38336600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr10:38307800-38343600	Weak transcription	Small Intestine	intestine
20	chr10:38307800-38344000	Weak transcription	Stomach Mucosa	stomach
21	chr10:38308000-38342200	Weak transcription	Brain Angular Gyrus	brain
22	chr10:38308600-38327800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr10:38309000-38326400	Strong transcription	Dnd41	blood
24	chr10:38309000-38327200	Weak transcription	Fetal Heart	heart
25	chr10:38309000-38339200	Weak transcription	HUVEC	blood vessel
26	chr10:38309000-38342200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr10:38309600-38325000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr10:38309800-38344200	Weak transcription	NH-A	brain
29	chr10:38310000-38324400	Weak transcription	HMEC	breast
30	chr10:38313800-38325600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr10:38313800-38326000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr10:38314000-38326800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr10:38314000-38327400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr10:38314200-38323000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr10:38314600-38342800	Weak transcription	Brain Substantia Nigra	brain
36	chr10:38315000-38323400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr10:38315000-38333800	Weak transcription	Esophagus	oesophagus
38	chr10:38315000-38342800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr10:38315800-38324200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr10:38315800-38327400	Strong transcription	Ovary	ovary
41	chr10:38316000-38323200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr10:38316000-38339800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr10:38316000-38342600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr10:38316600-38322800	Weak transcription	Brain Hippocampus Middle	brain
45	chr10:38316600-38323200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr10:38316600-38323400	Weak transcription	NHEK	skin
47	chr10:38316600-38324400	Weak transcription	Osteobl	bone
48	chr10:38316600-38334000	Weak transcription	K562	blood
49	chr10:38316600-38343600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr10:38316800-38326600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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