Variant report

Variant	rs11612002
Chromosome Location	chr12:50824232-50824233
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	chr12:50812613..50814185-chr12:50823081..50825818,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10459233	0.84[CEU][hapmap]
rs10783372	0.83[CEU][hapmap]
rs10783373	0.84[CEU][hapmap]
rs10876047	0.84[CEU][hapmap]
rs10876051	0.84[CEU][hapmap]
rs10876052	0.84[CEU][hapmap]
rs10876053	0.84[CEU][hapmap]
rs10876056	0.84[CEU][hapmap]
rs10876065	0.84[CEU][hapmap]
rs10876070	0.84[CEU][hapmap]
rs10876071	0.84[CEU][hapmap]
rs10876072	0.84[CEU][hapmap]
rs11169479	0.84[CEU][hapmap]
rs11169481	0.84[CEU][hapmap]
rs11169493	0.84[CEU][hapmap]
rs11169507	0.84[CEU][hapmap]
rs11613488	0.84[CEU][hapmap]
rs4131769	0.84[CEU][hapmap]
rs4238106	0.84[CEU][hapmap]
rs4768853	0.84[CEU][hapmap]
rs4768888	0.84[CEU][hapmap]
rs4768975	0.84[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7138604	0.84[CEU][hapmap]
rs7305375	0.84[CEU][hapmap]
rs7307419	0.84[CEU][hapmap]
rs7956591	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1054480	chr12:50691039-50859665	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1041563	chr12:50705715-50861699	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1049665	chr12:50705715-50871542	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv899076	chr12:50770291-50869589	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
7	nsv469376	chr12:50792846-50856613	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
8	nsv558841	chr12:50792846-50856613	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
9	nsv470291	chr12:50792846-50858820	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11612002	GPD1	cis	parietal	SCAN
rs11612002	ASB8	cis	cerebellum	SCAN
rs11612002	ZNF641	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50796800-50832600	Weak transcription	Brain Substantia Nigra	brain
2	chr12:50797600-50826200	Weak transcription	NHDF-Ad	bronchial
3	chr12:50797600-50826800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:50797600-50829600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:50809600-50872200	Weak transcription	Fetal Brain Male	brain
6	chr12:50810600-50824400	Weak transcription	NHLF	lung
7	chr12:50810600-50856600	Weak transcription	Aorta	Aorta
8	chr12:50812000-50827600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:50813400-50825600	Weak transcription	Primary T cells from cord blood	blood
10	chr12:50815800-50834400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:50819000-50824400	Strong transcription	K562	blood
12	chr12:50819200-50827200	Strong transcription	Fetal Intestine Small	intestine
13	chr12:50819200-50830200	Strong transcription	Fetal Stomach	stomach
14	chr12:50819200-50870800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:50819800-50830000	Weak transcription	Fetal Heart	heart
16	chr12:50819800-50842400	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr12:50819800-50867400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:50820000-50824600	Weak transcription	GM12878-XiMat	blood
19	chr12:50820000-50831600	Weak transcription	Psoas Muscle	Psoas
20	chr12:50820000-50835400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:50820000-50835600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:50820000-50841400	Weak transcription	Esophagus	oesophagus
23	chr12:50820000-50845400	Weak transcription	Right Atrium	heart
24	chr12:50820000-50867200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:50820200-50835200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:50820200-50869800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr12:50820200-50871000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:50820400-50830000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:50820600-50839400	Strong transcription	Fetal Thymus	thymus
30	chr12:50820600-50843400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:50820800-50839600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:50821000-50825000	Strong transcription	Liver	Liver
33	chr12:50821000-50839600	Strong transcription	Hela-S3	cervix
34	chr12:50821000-50841600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:50821000-50843000	Strong transcription	Placenta	Placenta
36	chr12:50821000-50850600	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr12:50821200-50830200	Strong transcription	Fetal Muscle Leg	muscle
38	chr12:50821200-50845000	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr12:50821200-50848200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr12:50821400-50845200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:50821600-50824600	Strong transcription	HSMM	muscle
42	chr12:50821600-50830000	Strong transcription	Left Ventricle	heart
43	chr12:50821600-50830200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:50821600-50830400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:50821600-50836200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:50821600-50836800	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:50821600-50836800	Strong transcription	A549	lung
48	chr12:50821600-50839600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:50821600-50839600	Strong transcription	Adipose Nuclei	Adipose
50	chr12:50821600-50842800	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links