Variant report

Variant	rs2148534
Chromosome Location	chr12:29761411-29761412
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	chr12:29760132..29762663-chr12:29763281..29765764,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10771553	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12372765	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1409615	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159699	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs159700	0.93[EUR][1000 genomes]
rs159712	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs159713	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs159716	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs167253	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1863224	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs213539	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2209660	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2209661	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2209662	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2225065	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2432958	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931205	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7959535	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7960236	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7960782	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7965227	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs994171	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:45 , 50 per page) page: 1

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	chr12:29736800-29762800	Weak transcription	Fetal Stomach	stomach
4	chr12:29737200-29761800	Weak transcription	Right Ventricle	heart
5	chr12:29737200-29762400	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:29737200-29762800	Weak transcription	Psoas Muscle	Psoas
7	chr12:29743200-29769800	Weak transcription	NHLF	lung
8	chr12:29744400-29790800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:29744600-29765400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:29744600-29791000	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:29744800-29764600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:29744800-29778200	Weak transcription	Ovary	ovary
13	chr12:29745200-29762000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:29746200-29762200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:29748600-29762600	Weak transcription	Spleen	Spleen
16	chr12:29750000-29762200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:29750400-29762600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:29752400-29761600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:29752600-29763000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr12:29752600-29763600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:29752600-29764600	Weak transcription	HSMMtube	muscle
22	chr12:29752600-29765600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:29752600-29768400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:29752600-29778200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:29752800-29762400	Weak transcription	Liver	Liver
26	chr12:29753600-29764800	Weak transcription	NHDF-Ad	bronchial
27	chr12:29755800-29763400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:29756200-29766000	Weak transcription	HSMM	muscle
29	chr12:29757000-29761600	Weak transcription	HMEC	breast
30	chr12:29757200-29761600	Weak transcription	Aorta	Aorta
31	chr12:29757200-29763400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:29757200-29766200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:29757400-29762200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:29757600-29765800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:29759000-29763600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr12:29760000-29762400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:29760400-29763400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:29760400-29787400	Weak transcription	Adipose Nuclei	Adipose
39	chr12:29760800-29761600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:29760800-29761600	Weak transcription	Left Ventricle	heart
41	chr12:29760800-29765400	Enhancers	Fetal Heart	heart
42	chr12:29760800-29767000	Weak transcription	Pancreas	Pancrea
43	chr12:29761000-29762200	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr12:29761200-29761800	Weak transcription	Right Atrium	heart
45	chr12:29761400-29761800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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