Variant report

Variant	rs17099883
Chromosome Location	chr12:64261099-64261100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64259856..64261721-chr12:64265461..64267447,2	MCF-7	breast:
2	chr12:64260075..64262066-chr12:64596655..64599026,2	MCF-7	breast:
3	chr12:64257945..64259859-chr12:64259892..64262492,3	MCF-7	breast:
4	chr12:64254678..64258025-chr12:64259314..64262432,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212298	Chromatin interaction
ENSG00000242087	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11175194	0.85[EUR][1000 genomes]
rs11175206	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs12229174	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12230811	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17099867	0.81[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17099869	0.85[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57082798	0.81[ASN][1000 genomes]
rs58282814	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73124618	0.87[EUR][1000 genomes]
rs73126620	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7963684	1.00[CEU][hapmap];0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2751110	chr12:63939733-64274680	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv1810729	chr12:64234926-64268005	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
5	esv1833454	chr12:64237504-64264837	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
6	esv1803717	chr12:64250221-64261249	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64241000-64261200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:64241000-64268800	Weak transcription	Lung	lung
3	chr12:64241000-64278800	Weak transcription	Fetal Stomach	stomach
4	chr12:64243400-64263000	Weak transcription	NHEK	skin
5	chr12:64244000-64263600	Weak transcription	Fetal Lung	lung
6	chr12:64246200-64286400	Weak transcription	Fetal Brain Female	brain
7	chr12:64247800-64268200	Weak transcription	Fetal Brain Male	brain
8	chr12:64250200-64287200	Weak transcription	Aorta	Aorta
9	chr12:64256600-64262200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:64256600-64263600	Weak transcription	HSMMtube	muscle
11	chr12:64256800-64262200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:64256800-64263200	Weak transcription	Right Atrium	heart
13	chr12:64256800-64271400	Weak transcription	Brain Angular Gyrus	brain
14	chr12:64256800-64276600	Weak transcription	HSMM	muscle
15	chr12:64256800-64282600	Weak transcription	Gastric	stomach
16	chr12:64257000-64262600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:64257000-64262800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:64257000-64263600	Weak transcription	NH-A	brain
19	chr12:64257400-64262000	Weak transcription	Left Ventricle	heart
20	chr12:64257400-64263200	Weak transcription	NHDF-Ad	bronchial
21	chr12:64257400-64270600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:64257800-64262800	Weak transcription	HMEC	breast
23	chr12:64258000-64262800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:64258000-64263000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr12:64258200-64262600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:64258200-64262800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:64258200-64263200	Weak transcription	NHLF	lung
28	chr12:64258400-64262800	Weak transcription	Osteobl	bone
29	chr12:64258400-64263000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:64258400-64263400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:64258600-64262400	Weak transcription	Hela-S3	cervix
32	chr12:64258600-64263000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:64258600-64263000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr12:64258800-64286200	Weak transcription	Fetal Intestine Small	intestine
35	chr12:64259000-64263000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:64259200-64266800	Weak transcription	Fetal Intestine Large	intestine
37	chr12:64259600-64261200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:64259600-64261400	Enhancers	A549	lung
39	chr12:64259600-64262000	Weak transcription	Pancreas	Pancrea
40	chr12:64259800-64265600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:64260000-64262800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:64260000-64263200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:64260200-64263200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr12:64260200-64263200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr12:64260200-64263400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr12:64260200-64264600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:64260400-64263400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:64260400-64263400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:64260600-64261200	Enhancers	Stomach Mucosa	stomach
50	chr12:64260800-64263200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links