Variant report

Variant	rs12134949
Chromosome Location	chr1:158002002-158002003
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	chr1:157987648..157990014-chr1:158000833..158002495,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10430456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12021619	1.00[CEU][hapmap]
rs12025305	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12037357	1.00[CEU][hapmap]
rs12039337	1.00[CEU][hapmap]
rs12118340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12118455	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12568166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16839617	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16839627	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16839630	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16839636	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1972216	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1980765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971179	0.81[JPT][hapmap]
rs4971180	0.81[JPT][hapmap]
rs4971181	0.89[ASN][1000 genomes]
rs4971182	0.89[ASN][1000 genomes]
rs4971183	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4971184	0.89[ASN][1000 genomes]
rs59530587	0.89[AFR][1000 genomes]
rs6661149	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6661160	0.89[ASN][1000 genomes]
rs6664509	0.89[ASN][1000 genomes]
rs6665788	0.96[ASN][1000 genomes]
rs6665898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6690504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6692314	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6699860	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73022620	0.90[AFR][1000 genomes]
rs7548850	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7555783	1.00[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823720	chr1:157978556-158034017	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:157985200-158006000	Weak transcription	Fetal Thymus	thymus
2	chr1:157989400-158007400	Weak transcription	Gastric	stomach
3	chr1:157991800-158002200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:157991800-158007400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:157993000-158007400	Weak transcription	HSMMtube	muscle
6	chr1:157993000-158007600	Weak transcription	Esophagus	oesophagus
7	chr1:157993200-158007400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:157995000-158007800	Weak transcription	Brain Germinal Matrix	brain
9	chr1:157995200-158004200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:157995400-158007600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:157995600-158004400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:157995800-158005600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:157995800-158007400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:157996000-158007400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:157996000-158007400	Weak transcription	Lung	lung
16	chr1:157996200-158006800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:157996200-158007600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:157996200-158007600	Weak transcription	Spleen	Spleen
19	chr1:157996400-158005600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:157996400-158007400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:157997200-158005600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:157997600-158004800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:157997600-158047600	Weak transcription	Dnd41	blood
24	chr1:157998000-158007400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:157998200-158007600	Weak transcription	Left Ventricle	heart
26	chr1:157999000-158006200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:157999000-158013000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:157999200-158005000	Weak transcription	Ovary	ovary
29	chr1:157999400-158005400	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:157999400-158005400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:158000000-158002400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:158000200-158002200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:158000200-158002200	Strong transcription	Fetal Intestine Small	intestine
34	chr1:158000200-158002800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:158000200-158002800	Strong transcription	Osteobl	bone
36	chr1:158000200-158004000	Strong transcription	Fetal Stomach	stomach
37	chr1:158000200-158004400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:158000400-158002400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:158000400-158002400	Strong transcription	NHEK	skin
40	chr1:158000400-158002600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr1:158000400-158002600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:158000600-158002200	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr1:158000600-158002200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:158000600-158002200	Strong transcription	Hela-S3	cervix
45	chr1:158000600-158002400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:158000600-158002400	Strong transcription	Fetal Muscle Leg	muscle
47	chr1:158000600-158002800	Strong transcription	NHLF	lung
48	chr1:158000800-158002200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:158000800-158003600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:158001000-158002200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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