Variant report

Variant	rs7959989
Chromosome Location	chr12:31814741-31814742
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31812744..31814749-chr12:31824204..31825895,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10843992	0.87[ASN][1000 genomes]
rs11051514	0.85[ASN][1000 genomes]
rs11051515	0.87[ASN][1000 genomes]
rs11051516	0.87[ASN][1000 genomes]
rs11051517	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11051519	0.94[ASN][1000 genomes]
rs11051521	0.84[AMR][1000 genomes]
rs11051522	0.84[AMR][1000 genomes]
rs11051527	0.90[ASN][1000 genomes]
rs11051534	0.90[ASN][1000 genomes]
rs11051535	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11051536	0.89[ASN][1000 genomes]
rs11051538	0.89[ASN][1000 genomes]
rs11051540	0.85[ASN][1000 genomes]
rs11051546	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11051547	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12231666	0.84[ASN][1000 genomes]
rs4931536	0.94[ASN][1000 genomes]
rs4931538	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4931545	0.86[ASN][1000 genomes]
rs4931546	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4931547	0.86[ASN][1000 genomes]
rs59091295	0.82[ASN][1000 genomes]
rs61561194	0.87[ASN][1000 genomes]
rs61932065	0.84[ASN][1000 genomes]
rs7308889	0.88[ASN][1000 genomes]
rs7316528	0.87[ASN][1000 genomes]
rs7955365	0.90[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	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv898966	chr12:31810126-31944985	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31812800-31818000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:31812800-31818000	Weak transcription	Spleen	Spleen
3	chr12:31812800-31818200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:31812800-31819600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:31812800-31823800	Weak transcription	Small Intestine	intestine
6	chr12:31813000-31814800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:31813000-31814800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:31813000-31814800	Weak transcription	Lung	lung
9	chr12:31813000-31815800	Enhancers	Primary B cells from peripheral blood	blood
10	chr12:31813000-31815800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:31813000-31816800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:31813000-31817200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:31813000-31822000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:31813000-31822000	Weak transcription	NH-A	brain
15	chr12:31813000-31826000	Weak transcription	Gastric	stomach
16	chr12:31813200-31816800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:31813200-31817000	Weak transcription	Fetal Kidney	kidney
18	chr12:31813200-31818000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:31813200-31818000	Weak transcription	Placenta	Placenta
20	chr12:31813200-31818400	Weak transcription	Esophagus	oesophagus
21	chr12:31813200-31822000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:31813200-31837000	Weak transcription	Fetal Brain Male	brain
23	chr12:31813400-31814800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:31813400-31814800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:31813400-31814800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:31813400-31814800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr12:31813400-31814800	Weak transcription	Fetal Muscle Leg	muscle
28	chr12:31813400-31814800	Weak transcription	Fetal Stomach	stomach
29	chr12:31813400-31814800	Weak transcription	Left Ventricle	heart
30	chr12:31813400-31814800	Weak transcription	Pancreas	Pancrea
31	chr12:31813400-31814800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:31813400-31814800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr12:31813400-31814800	Weak transcription	GM12878-XiMat	blood
34	chr12:31813400-31815000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr12:31813400-31815000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:31813400-31815000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:31813400-31815000	Weak transcription	Fetal Intestine Small	intestine
38	chr12:31813400-31815200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:31813400-31815200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr12:31813400-31815200	Weak transcription	Brain Substantia Nigra	brain
41	chr12:31813400-31816400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:31813400-31816400	Weak transcription	HepG2	liver
43	chr12:31813400-31816600	Weak transcription	NHLF	lung
44	chr12:31813400-31816800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:31813400-31818800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:31813400-31820600	Weak transcription	HSMMtube	muscle
47	chr12:31813400-31820800	Weak transcription	Ovary	ovary
48	chr12:31813400-31821600	Weak transcription	Thymus	Thymus
49	chr12:31813400-31821800	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr12:31813400-31821800	Weak transcription	Colon Smooth Muscle	Colon

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