Variant report

Variant	rs994172
Chromosome Location	chr12:29770255-29770256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29765447..29767500-chr12:29770091..29771858,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10400541	0.86[CHB][hapmap]
rs10771545	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs10771546	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs10771547	0.91[JPT][hapmap]
rs11050270	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs11050271	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs11050273	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11050278	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs11050280	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11050292	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs11050293	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs11050297	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs11050299	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs11050300	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs11050301	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs11050302	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs11050319	0.95[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11611194	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs12368037	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12371221	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12579805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581671	0.90[JPT][hapmap]
rs12819780	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326758	0.86[CHB][hapmap]
rs1409616	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]
rs1409617	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs159696	0.86[CHB][hapmap]
rs159701	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs159703	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs159704	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs159705	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs159707	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs159708	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159709	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs159714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159715	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1988548	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2182547	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288131	0.81[CHB][hapmap]
rs2288132	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs2288133	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs2478469	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2478470	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2553077	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2766605	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]
rs2766606	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]
rs299455	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs299456	0.82[CHB][hapmap]
rs299459	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs4931201	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7294502	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs7295284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7301491	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7310555	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs7310895	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs7314549	0.91[JPT][hapmap]
rs9300191	0.91[JPT][hapmap]

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	chr12:29744400-29790800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:29744600-29791000	Weak transcription	Fetal Muscle Leg	muscle
3	chr12:29744800-29778200	Weak transcription	Ovary	ovary
4	chr12:29752600-29778200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:29760400-29787400	Weak transcription	Adipose Nuclei	Adipose
6	chr12:29761800-29778000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:29762600-29770400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:29763000-29777400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:29763000-29777600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:29763200-29777600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:29763800-29773000	Weak transcription	Left Ventricle	heart
12	chr12:29763800-29778000	Weak transcription	Fetal Stomach	stomach
13	chr12:29763800-29786800	Weak transcription	Spleen	Spleen
14	chr12:29763800-29793600	Weak transcription	Right Ventricle	heart
15	chr12:29765000-29780800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:29765000-29786800	Weak transcription	HSMMtube	muscle
17	chr12:29765200-29770800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:29765200-29773600	Weak transcription	Right Atrium	heart
19	chr12:29765200-29777600	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:29765200-29778200	Weak transcription	Aorta	Aorta
21	chr12:29765200-29785400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:29765400-29777400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:29765400-29777400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr12:29765400-29780800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr12:29765600-29802600	Weak transcription	Psoas Muscle	Psoas
26	chr12:29766000-29770400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:29766400-29778600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:29766800-29773800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:29767600-29778000	Weak transcription	Fetal Kidney	kidney
30	chr12:29768200-29770400	Weak transcription	HSMM	muscle
31	chr12:29768800-29776400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:29769400-29770600	Enhancers	NHDF-Ad	bronchial
33	chr12:29769400-29771600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:29769600-29770800	Enhancers	NHEK	skin
35	chr12:29769600-29770800	Enhancers	Osteobl	bone
36	chr12:29769600-29771000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:29769600-29771000	Enhancers	Hela-S3	cervix
38	chr12:29769600-29771200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:29769600-29771200	Enhancers	HMEC	breast
40	chr12:29769800-29770400	Enhancers	NHLF	lung
41	chr12:29769800-29770600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:29769800-29770800	Enhancers	NH-A	brain
43	chr12:29769800-29771000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:29769800-29772600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:29769800-29778400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:29770000-29770800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr12:29770000-29771000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:29770200-29770600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:29770200-29770600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:29770200-29770600	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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