Variant report

Variant	rs11172134
Chromosome Location	chr12:57645789-57645790
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57645713-57646126	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57637406..57639155-chr12:57645577..57649504,4	K562	blood:
2	chr12:57640540..57643172-chr12:57644604..57647826,3	K562	blood:
3	chr12:57641844..57643459-chr12:57645727..57647694,2	MCF-7	breast:
4	chr12:57607877..57611743-chr12:57643490..57646687,3	K562	blood:
5	chr12:57637439..57639155-chr12:57645577..57647723,2	K562	blood:

No data

Variant related genes	Relation type
STAC3	TF binding region
ENSG00000182379	Chromatin interaction
ENSG00000185482	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1106766	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11172147	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11172181	0.81[AMR][1000 genomes]
rs11609805	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs11612551	1.00[JPT][hapmap]
rs11614506	0.89[CHB][hapmap]
rs12313306	0.81[AMR][1000 genomes]
rs12313762	0.92[AMR][1000 genomes]
rs3741414	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs4760254	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs4760278	0.89[CHB][hapmap]
rs4760355	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs540730	1.00[CHB][hapmap]
rs56205943	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7397189	0.82[AMR][1000 genomes]
rs7964492	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57637200-57647400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:57637200-57648400	Weak transcription	Brain Angular Gyrus	brain
3	chr12:57637400-57647200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:57637600-57648400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:57637600-57648400	Weak transcription	Lung	lung
6	chr12:57637600-57649000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:57637600-57649600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:57637600-57651200	Weak transcription	NHDF-Ad	bronchial
9	chr12:57637600-57654200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:57637800-57645800	Weak transcription	Osteobl	bone
11	chr12:57637800-57648400	Weak transcription	Spleen	Spleen
12	chr12:57637800-57649800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:57638000-57647000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:57638000-57647200	Weak transcription	Fetal Brain Female	brain
15	chr12:57638000-57648200	Weak transcription	Primary T cells from cord blood	blood
16	chr12:57638000-57648400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:57638000-57648400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:57638000-57648400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:57638000-57648400	Weak transcription	Brain Anterior Caudate	brain
20	chr12:57638000-57648400	Weak transcription	Pancreas	Pancrea
21	chr12:57638000-57649000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:57638000-57649000	Weak transcription	Dnd41	blood
23	chr12:57638000-57649400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:57638000-57649400	Weak transcription	Fetal Heart	heart
25	chr12:57638000-57649600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr12:57638000-57649600	Weak transcription	Right Ventricle	heart
27	chr12:57638000-57651200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:57638000-57651200	Weak transcription	Fetal Brain Male	brain
29	chr12:57638200-57648000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:57638200-57648400	Weak transcription	Colonic Mucosa	Colon
31	chr12:57638400-57648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:57638600-57649600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:57638800-57673600	Weak transcription	Stomach Mucosa	stomach
34	chr12:57639000-57647000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:57639000-57647000	Weak transcription	Fetal Intestine Small	intestine
36	chr12:57639000-57648000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:57639000-57648000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:57639200-57647200	Weak transcription	Fetal Stomach	stomach
39	chr12:57639200-57648200	Weak transcription	Brain Germinal Matrix	brain
40	chr12:57639200-57648400	Weak transcription	Liver	Liver
41	chr12:57639200-57648400	Weak transcription	Placenta	Placenta
42	chr12:57639200-57648600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:57639600-57649800	Weak transcription	A549	lung
44	chr12:57639600-57651200	Weak transcription	Hela-S3	cervix
45	chr12:57639600-57651200	Weak transcription	HepG2	liver
46	chr12:57640600-57649200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr12:57640800-57646800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr12:57641000-57649200	Weak transcription	Fetal Lung	lung
49	chr12:57641000-57649800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:57641800-57648400	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links