Variant report

Variant	rs1409616
Chromosome Location	chr12:29764402-29764403
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr12:29764402-29764557	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29760132..29762663-chr12:29763281..29765764,2	MCF-7	breast:

Variant related genes	Relation type
TMTC1	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10400541	0.86[CHB][hapmap]
rs10771545	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs10771546	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs10771547	0.95[JPT][hapmap]
rs11050270	0.80[CHB][hapmap];0.96[JPT][hapmap]
rs11050271	0.82[CHB][hapmap];0.96[JPT][hapmap]
rs11050273	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11050278	0.82[CHB][hapmap];0.96[JPT][hapmap]
rs11050280	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11050292	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11050293	0.85[CHB][hapmap];0.96[JPT][hapmap]
rs11050297	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs11050299	0.86[CHB][hapmap];0.96[JPT][hapmap]
rs11050300	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11050301	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11050302	0.86[CHB][hapmap];0.96[JPT][hapmap];0.80[ASN][1000 genomes]
rs11050319	0.95[CEU][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11611194	0.82[CHB][hapmap];0.96[JPT][hapmap]
rs12368037	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12371221	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs12579805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12581671	0.95[JPT][hapmap]
rs12819780	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1326758	0.86[CHB][hapmap]
rs1409617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159696	0.86[CHB][hapmap]
rs159701	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs159703	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs159704	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs159705	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs159707	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs159708	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs159709	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs159714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs159715	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1988548	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2113879	0.83[JPT][hapmap]
rs2113880	0.83[JPT][hapmap]
rs2182547	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288131	0.81[CHB][hapmap]
rs2288132	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2288133	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2350532	0.83[JPT][hapmap]
rs2478469	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2478470	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2553077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2766605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2766606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299455	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs299456	0.81[CHB][hapmap]
rs299459	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs299463	0.81[JPT][hapmap]
rs299465	0.83[JPT][hapmap]
rs299472	0.83[JPT][hapmap]
rs299475	0.81[JPT][hapmap]
rs4931201	0.82[CHB][hapmap];0.96[JPT][hapmap]
rs7294502	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7295284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7301491	0.82[CHB][hapmap];0.96[JPT][hapmap]
rs7310555	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7310895	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7314549	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs9300191	0.95[JPT][hapmap]
rs9738399	0.81[ASN][1000 genomes]
rs994172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1053629	chr12:29680163-29826626	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1051913	chr12:29741676-29770807	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv870004	chr12:29762415-29825798	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29716200-29764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:29731800-29769600	Weak transcription	Hela-S3	cervix
3	chr12:29743200-29769800	Weak transcription	NHLF	lung
4	chr12:29744400-29790800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:29744600-29765400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:29744600-29791000	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:29744800-29764600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:29744800-29778200	Weak transcription	Ovary	ovary
9	chr12:29752600-29764600	Weak transcription	HSMMtube	muscle
10	chr12:29752600-29765600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:29752600-29768400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:29752600-29778200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:29753600-29764800	Weak transcription	NHDF-Ad	bronchial
14	chr12:29756200-29766000	Weak transcription	HSMM	muscle
15	chr12:29757200-29766200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:29757600-29765800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:29760400-29787400	Weak transcription	Adipose Nuclei	Adipose
18	chr12:29760800-29765400	Enhancers	Fetal Heart	heart
19	chr12:29760800-29767000	Weak transcription	Pancreas	Pancrea
20	chr12:29761800-29778000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:29762400-29765200	Enhancers	Liver	Liver
22	chr12:29762400-29765200	Enhancers	Colon Smooth Muscle	Colon
23	chr12:29762400-29769600	Weak transcription	HMEC	breast
24	chr12:29762600-29770400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:29762800-29765400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:29762800-29770000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr12:29763000-29777400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:29763000-29777600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:29763200-29764600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:29763200-29764800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr12:29763200-29764800	Weak transcription	Psoas Muscle	Psoas
32	chr12:29763200-29766400	Enhancers	Osteobl	bone
33	chr12:29763200-29777600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:29763400-29764600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr12:29763400-29764800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:29763400-29766200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:29763400-29766600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:29763600-29765000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr12:29763600-29765200	Enhancers	Rectal Smooth Muscle	rectum
40	chr12:29763800-29764600	Weak transcription	Aorta	Aorta
41	chr12:29763800-29764800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:29763800-29764800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:29763800-29765000	Weak transcription	Gastric	stomach
44	chr12:29763800-29773000	Weak transcription	Left Ventricle	heart
45	chr12:29763800-29778000	Weak transcription	Fetal Stomach	stomach
46	chr12:29763800-29786800	Weak transcription	Spleen	Spleen
47	chr12:29763800-29793600	Weak transcription	Right Ventricle	heart
48	chr12:29764000-29764600	Weak transcription	Right Atrium	heart
49	chr12:29764000-29764800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:29764200-29765400	Enhancers	Stomach Smooth Muscle	stomach

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