Variant report

Variant	rs11139778
Chromosome Location	chr9:85397317-85397318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:85389992..85391848-chr9:85397163..85400021,3	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10867880	0.96[ASN][1000 genomes]
rs11139733	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11139734	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11139735	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11139736	0.86[ASN][1000 genomes]
rs11139737	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11139755	0.95[ASN][1000 genomes]
rs11139756	0.95[ASN][1000 genomes]
rs11139757	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11139763	0.89[ASN][1000 genomes]
rs11139764	0.94[ASN][1000 genomes]
rs11139765	0.97[ASN][1000 genomes]
rs11139767	0.97[ASN][1000 genomes]
rs11139768	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11139772	0.97[ASN][1000 genomes]
rs11139773	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11139774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11139775	1.00[ASN][1000 genomes]
rs11139777	1.00[ASN][1000 genomes]
rs11139781	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11139783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11139784	0.99[ASN][1000 genomes]
rs11139785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11562396	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12238605	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61035164	0.95[ASN][1000 genomes]
rs7039347	1.00[ASN][1000 genomes]
rs73477989	0.95[ASN][1000 genomes]
rs73477996	0.95[ASN][1000 genomes]
rs73478001	0.95[ASN][1000 genomes]
rs7853662	0.91[ASN][1000 genomes]
rs7865518	0.91[ASN][1000 genomes]
rs7865827	0.95[ASN][1000 genomes]
rs7867099	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7869282	0.88[ASN][1000 genomes]
rs7869890	0.95[ASN][1000 genomes]
rs7870272	0.95[ASN][1000 genomes]
rs7871433	0.91[ASN][1000 genomes]
rs7873765	0.88[ASN][1000 genomes]
rs7875501	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428539	chr9:85240027-85402367	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1035314	chr9:85348780-85549246	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv540161	chr9:85348780-85549246	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1039930	chr9:85349993-85536746	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv518664	chr9:85391686-85399923	Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85390800-85400600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
2	chr9:85391600-85404000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr9:85393400-85403800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:85395400-85401400	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:85395400-85424800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:85396200-85398000	Enhancers	Dnd41	blood
7	chr9:85396200-85398800	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr9:85396400-85397400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr9:85396600-85397600	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr9:85396600-85397800	Enhancers	Brain Germinal Matrix	brain
11	chr9:85396800-85397600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr9:85396800-85397600	Enhancers	Small Intestine	intestine
13	chr9:85396800-85397800	Enhancers	Duodenum Mucosa	Duodenum
14	chr9:85396800-85398000	Enhancers	Fetal Lung	lung
15	chr9:85397000-85397800	Enhancers	Fetal Brain Female	brain
16	chr9:85397000-85397800	Enhancers	Fetal Intestine Small	intestine
17	chr9:85397000-85397800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr9:85397200-85397400	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr9:85397200-85397400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr9:85397200-85397400	Flanking Active TSS	Fetal Brain Male	brain
21	chr9:85397200-85398200	Enhancers	Fetal Kidney	kidney
22	chr9:85397200-85398600	Enhancers	Stomach Mucosa	stomach

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