Variant report

Variant	rs7903649
Chromosome Location	chr10:52360372-52360373
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52356810..52366659-chr10:52378806..52385975,25	MCF-7	breast:
2	chr10:52359953..52362709-chr10:52369369..52373300,4	MCF-7	breast:
3	chr10:52337504..52344093-chr10:52356709..52361052,9	K562	blood:
4	chr10:52358660..52367648-chr10:52378481..52386533,25	MCF-7	breast:
5	chr10:52359176..52361319-chr10:52370214..52372763,2	K562	blood:
6	chr10:52359176..52362800-chr10:52370214..52372763,3	K562	blood:
7	chr10:52359260..52360848-chr10:52387112..52388927,2	K562	blood:
8	chr10:52355521..52357816-chr10:52359729..52362613,2	MCF-7	breast:
9	chr10:52351092..52355625-chr10:52355822..52361152,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10740762	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]
rs10763590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10826242	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11006259	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3001879	0.91[EUR][1000 genomes]
rs3001883	1.00[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs3001885	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3011714	0.91[EUR][1000 genomes]
rs4268459	0.94[EUR][1000 genomes]
rs4935734	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4935735	1.00[CEU][hapmap];0.81[YRI][hapmap];0.90[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];0.96[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]
rs4935739	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6481442	1.00[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6481461	1.00[CEU][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs7067552	1.00[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs7073182	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7089882	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs7090996	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7094655	0.89[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];0.94[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];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7908136	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7909486	1.00[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7918559	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv8661	chr10:52356909-52360389	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7903649	CSTF2T	cis	parietal	SCAN
rs7903649	ARHGAP22	cis	parietal	SCAN
rs7903649	PIK3C2B	trans	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

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	chr10:52343400-52360600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr10:52343600-52362200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr10:52346600-52363400	Weak transcription	Adipose Nuclei	Adipose
9	chr10:52346600-52363800	Weak transcription	Spleen	Spleen
10	chr10:52346800-52360600	Weak transcription	HUVEC	blood vessel
11	chr10:52348000-52363400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr10:52348400-52363000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr10:52349000-52363200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr10:52349200-52360400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr10:52349200-52363200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr10:52349400-52363000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr10:52349400-52363000	Weak transcription	Lung	lung
18	chr10:52349600-52360600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr10:52349600-52360600	Weak transcription	Thymus	Thymus
20	chr10:52349600-52361800	Weak transcription	Esophagus	oesophagus
21	chr10:52349600-52363600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr10:52349600-52364000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr10:52349600-52364800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr10:52349800-52362600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr10:52349800-52362600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr10:52349800-52362800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr10:52349800-52363000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr10:52349800-52363800	Weak transcription	Primary B cells from cord blood	blood
29	chr10:52350000-52360400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr10:52350000-52360600	Weak transcription	Primary T cells from cord blood	blood
31	chr10:52354000-52361600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr10:52354200-52360400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr10:52354200-52362200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr10:52354200-52362600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr10:52354200-52362800	Weak transcription	Fetal Brain Male	brain
36	chr10:52355600-52361800	Weak transcription	Right Atrium	heart
37	chr10:52356400-52361400	Genic enhancers	K562	blood
38	chr10:52356600-52363800	Weak transcription	Fetal Brain Female	brain
39	chr10:52356800-52363400	Weak transcription	Colon Smooth Muscle	Colon
40	chr10:52357200-52361200	Weak transcription	Liver	Liver
41	chr10:52358200-52362800	Enhancers	Fetal Heart	heart
42	chr10:52358400-52367000	Enhancers	Fetal Lung	lung
43	chr10:52358600-52360600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr10:52358600-52361000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr10:52358600-52361400	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr10:52358600-52362200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr10:52358800-52362200	Weak transcription	HepG2	liver
48	chr10:52358800-52367800	Enhancers	Brain Hippocampus Middle	brain
49	chr10:52359200-52360600	Enhancers	Placenta Amnion	Placenta Amnion
50	chr10:52359200-52361000	Enhancers	Placenta	Placenta

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