Variant report

Variant	rs12911648
Chromosome Location	chr15:33196270-33196271
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:33194367..33197072-chr15:33201375..33203984,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11632769	0.86[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11633201	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11634576	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12708498	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12902241	0.91[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12904870	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12916094	0.81[CHD][hapmap]
rs1376791	0.83[CEU][hapmap]
rs1470677	0.83[CEU][hapmap]
rs1470678	0.87[CEU][hapmap]
rs2122436	0.87[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2339164	0.82[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs347914	0.91[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs347915	0.87[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs347921	0.91[CEU][hapmap]
rs347922	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs347951	0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs347952	0.87[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs43768	0.87[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7178175	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7178325	0.91[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7180533	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8027183	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422296	chr15:32798938-33221215	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv832962	chr15:33111517-33239736	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv903978	chr15:33144202-33308641	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1041609	chr15:33148035-33355999	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv542339	chr15:33148035-33355999	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv903980	chr15:33149087-33264201	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv568917	chr15:33167171-33304172	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12911648	GABRA5	cis	parietal	SCAN
rs12911648	FAN1	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33149000-33202000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr15:33154400-33216800	Weak transcription	Fetal Thymus	thymus
3	chr15:33155000-33208200	Weak transcription	Fetal Kidney	kidney
4	chr15:33160000-33201800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:33162200-33202400	Weak transcription	Gastric	stomach
6	chr15:33166000-33202400	Weak transcription	Pancreas	Pancrea
7	chr15:33166200-33211800	Weak transcription	HSMMtube	muscle
8	chr15:33170800-33200400	Weak transcription	NH-A	brain
9	chr15:33178800-33197600	Weak transcription	Osteobl	bone
10	chr15:33179000-33198000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr15:33180600-33196600	Weak transcription	Placenta	Placenta
12	chr15:33181800-33198800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:33181800-33201000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:33182000-33200600	Weak transcription	Fetal Stomach	stomach
15	chr15:33191000-33201000	Weak transcription	Esophagus	oesophagus
16	chr15:33191000-33210800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:33191600-33196400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr15:33191600-33197600	Weak transcription	Lung	lung
19	chr15:33191800-33200000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:33191800-33214600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:33192000-33196600	Weak transcription	A549	lung
22	chr15:33192000-33197600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:33192000-33200000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:33192400-33197600	Weak transcription	Thymus	Thymus
25	chr15:33192400-33201400	Weak transcription	HSMM	muscle
26	chr15:33192400-33210600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:33192600-33197600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:33192600-33210800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:33193000-33197600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:33193000-33200400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:33194600-33200400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr15:33194800-33196800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:33194800-33200200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr15:33195000-33200200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr15:33195000-33215000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr15:33195200-33200200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:33195200-33200200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:33195400-33200200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:33195600-33197200	Enhancers	Primary B cells from peripheral blood	blood
40	chr15:33195800-33196600	Strong transcription	NHLF	lung
41	chr15:33195800-33197000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr15:33195800-33197600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:33196000-33197200	Enhancers	Primary B cells from cord blood	blood
44	chr15:33196200-33196800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr15:33196200-33196800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:33196200-33197000	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr15:33196200-33198200	Strong transcription	Sigmoid Colon	Sigmoid Colon

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