Variant report

Variant	rs10740762
Chromosome Location	chr10:52361844-52361845
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52335773..52337467-chr10:52361237..52363170,2	K562	blood:
2	chr10:52361423..52364078-chr10:52378639..52381362,2	K562	blood:
3	chr10:52356810..52366659-chr10:52378806..52385975,25	MCF-7	breast:
4	chr10:52359953..52362709-chr10:52369369..52373300,4	MCF-7	breast:
5	chr10:52358660..52367648-chr10:52378481..52386533,25	MCF-7	breast:
6	chr10:52359176..52362800-chr10:52370214..52372763,3	K562	blood:
7	chr10:52355521..52357816-chr10:52359729..52362613,2	MCF-7	breast:
8	chr10:52352876..52355415-chr10:52360770..52364645,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10763590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10826242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006259	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3001879	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3001883	1.00[CEU][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3001885	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3011714	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4268459	0.94[EUR][1000 genomes]
rs4935734	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4935735	1.00[CEU][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4935736	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];0.95[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];1.00[ASN][1000 genomes]
rs4935739	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6481442	1.00[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6481461	1.00[CEU][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7067552	1.00[CEU][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7073182	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7089882	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs7090996	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7094655	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7097359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7903649	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];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7904101	1.00[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7908136	0.95[EUR][1000 genomes]
rs7909486	1.00[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7918559	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10740762	CSTF2T	cis	parietal	SCAN
rs10740762	PIK3C2B	trans	parietal	SCAN
rs10740762	ARHGAP22	cis	parietal	SCAN
rs10740762	FLJ31958	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52336800-52363000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:52338000-52363800	Weak transcription	Fetal Kidney	kidney
3	chr10:52338000-52367000	Weak transcription	Aorta	Aorta
4	chr10:52341200-52373000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr10:52341800-52362000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr10:52343600-52362200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:52346600-52363400	Weak transcription	Adipose Nuclei	Adipose
8	chr10:52346600-52363800	Weak transcription	Spleen	Spleen
9	chr10:52348000-52363400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr10:52348400-52363000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr10:52349000-52363200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr10:52349200-52363200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr10:52349400-52363000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:52349400-52363000	Weak transcription	Lung	lung
15	chr10:52349600-52363600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr10:52349600-52364000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr10:52349600-52364800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr10:52349800-52362600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr10:52349800-52362600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr10:52349800-52362800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr10:52349800-52363000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr10:52349800-52363800	Weak transcription	Primary B cells from cord blood	blood
23	chr10:52354200-52362200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr10:52354200-52362600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr10:52354200-52362800	Weak transcription	Fetal Brain Male	brain
26	chr10:52356600-52363800	Weak transcription	Fetal Brain Female	brain
27	chr10:52356800-52363400	Weak transcription	Colon Smooth Muscle	Colon
28	chr10:52358200-52362800	Enhancers	Fetal Heart	heart
29	chr10:52358400-52367000	Enhancers	Fetal Lung	lung
30	chr10:52358600-52362200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr10:52358800-52362200	Weak transcription	HepG2	liver
32	chr10:52358800-52367800	Enhancers	Brain Hippocampus Middle	brain
33	chr10:52359400-52362200	Enhancers	HSMM	muscle
34	chr10:52359400-52369200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr10:52359600-52362400	Enhancers	HMEC	breast
36	chr10:52359600-52363600	Enhancers	A549	lung
37	chr10:52359600-52363800	Enhancers	NHDF-Ad	bronchial
38	chr10:52359800-52362200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr10:52359800-52362200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr10:52359800-52362400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr10:52359800-52363200	Weak transcription	Osteobl	bone
42	chr10:52359800-52363800	Enhancers	NHEK	skin
43	chr10:52360000-52362000	Weak transcription	Ovary	ovary
44	chr10:52360000-52366200	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr10:52360200-52362800	Enhancers	Right Ventricle	heart
46	chr10:52360200-52363000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr10:52360200-52375600	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr10:52360400-52362200	Weak transcription	Fetal Intestine Large	intestine
49	chr10:52360400-52366000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr10:52360600-52362000	Enhancers	Primary T cells from cord blood	blood

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