Variant report

Variant	rs12295206
Chromosome Location	chr11:73600351-73600352
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	chr11:73600327..73602691-chr11:73608708..73610968,2	MCF-7	breast:
2	chr11:73585766..73589510-chr11:73599101..73602813,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181924	Chromatin interaction
ENSG00000175575	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1122373	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11235909	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11235921	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11235924	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11235940	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11235941	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11235944	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11235948	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs11235956	0.91[ASN][1000 genomes]
rs11828006	0.83[ASN][1000 genomes]
rs12269892	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12280222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12284235	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs12284670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12287418	0.90[ASN][1000 genomes]
rs12291665	0.91[ASN][1000 genomes]
rs12294934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420040	0.92[ASN][1000 genomes]
rs12577447	0.83[ASN][1000 genomes]
rs1670539	1.00[CHB][hapmap]
rs17132368	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17132495	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs2010583	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2067913	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs3741138	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs3741139	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs56006060	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56380005	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58695771	0.98[ASN][1000 genomes]
rs59716840	0.83[ASN][1000 genomes]
rs637028	0.93[CHD][hapmap]
rs7111424	0.83[ASN][1000 genomes]
rs7116620	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7119602	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73549968	0.94[ASN][1000 genomes]
rs935985	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs935988	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[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	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv530641	chr11:73358393-73638725	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv1038105	chr11:73552023-73673836	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1035977	chr11:73581224-73617653	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73588600-73610200	Weak transcription	Gastric	stomach
2	chr11:73588600-73610200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:73588600-73611200	Weak transcription	Aorta	Aorta
4	chr11:73588800-73600600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr11:73588800-73600800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:73588800-73604200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:73588800-73604800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr11:73588800-73606200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr11:73588800-73607000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr11:73588800-73610200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:73588800-73610600	Weak transcription	Spleen	Spleen
12	chr11:73588800-73610800	Weak transcription	Lung	lung
13	chr11:73588800-73610800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr11:73588800-73611200	Weak transcription	Right Ventricle	heart
15	chr11:73588800-73622000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr11:73588800-73623000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr11:73588800-73625200	Weak transcription	Small Intestine	intestine
18	chr11:73588800-73630000	Weak transcription	Colonic Mucosa	Colon
19	chr11:73588800-73630200	Weak transcription	HUVEC	blood vessel
20	chr11:73589000-73602600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:73589000-73606000	Weak transcription	A549	lung
22	chr11:73589000-73610000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr11:73589000-73610200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:73589000-73610200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:73589000-73630200	Weak transcription	Fetal Brain Male	brain
26	chr11:73589200-73600800	Weak transcription	NHEK	skin
27	chr11:73589200-73601200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:73589200-73601200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:73589200-73611200	Weak transcription	Brain Substantia Nigra	brain
30	chr11:73589400-73600600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr11:73589400-73600600	Weak transcription	Brain Anterior Caudate	brain
32	chr11:73589400-73609800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr11:73589400-73610000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr11:73589400-73629200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:73589600-73603400	Weak transcription	Fetal Kidney	kidney
36	chr11:73590000-73610200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:73590000-73611200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:73591200-73602600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr11:73591200-73610200	Weak transcription	Pancreas	Pancrea
40	chr11:73591400-73605600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:73591400-73610200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:73591400-73610200	Weak transcription	Esophagus	oesophagus
43	chr11:73591600-73618000	Weak transcription	K562	blood
44	chr11:73594200-73603800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr11:73595200-73600600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr11:73595600-73604200	Weak transcription	Thymus	Thymus
47	chr11:73595600-73610200	Weak transcription	Ovary	ovary
48	chr11:73595800-73601200	Weak transcription	Brain Germinal Matrix	brain
49	chr11:73596000-73640800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr11:73597000-73601000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links