Variant report

Variant	rs6690504
Chromosome Location	chr1:158005657-158005658
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	chr1:157961376..157963058-chr1:158005272..158006485,12	MCF-7	breast:
2	chr1:157998908..158001801-chr1:158002681..158007266,4	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10430456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12021619	1.00[CEU][hapmap]
rs12025305	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118455	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134949	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]
rs12568166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16839617	1.00[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes]
rs16839627	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16839630	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16839636	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1972216	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1980765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971179	0.81[JPT][hapmap]
rs4971180	0.81[JPT][hapmap]
rs4971181	0.88[ASN][1000 genomes]
rs4971182	0.88[ASN][1000 genomes]
rs4971183	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4971184	0.88[ASN][1000 genomes]
rs6661149	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6661160	0.88[ASN][1000 genomes]
rs6664509	0.88[ASN][1000 genomes]
rs6665788	0.98[ASN][1000 genomes]
rs6665898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6692314	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699860	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7548850	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[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	chr1:157991800-158007400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:157993000-158007400	Weak transcription	HSMMtube	muscle
5	chr1:157993000-158007600	Weak transcription	Esophagus	oesophagus
6	chr1:157993200-158007400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:157995000-158007800	Weak transcription	Brain Germinal Matrix	brain
8	chr1:157995400-158007600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:157995800-158007400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:157996000-158007400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:157996000-158007400	Weak transcription	Lung	lung
12	chr1:157996200-158006800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:157996200-158007600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:157996200-158007600	Weak transcription	Spleen	Spleen
15	chr1:157996400-158007400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:157997600-158047600	Weak transcription	Dnd41	blood
17	chr1:157998000-158007400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:157998200-158007600	Weak transcription	Left Ventricle	heart
19	chr1:157999000-158006200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:157999000-158013000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:158001200-158011800	Weak transcription	Fetal Intestine Large	intestine
22	chr1:158001200-158047400	Weak transcription	Thymus	Thymus
23	chr1:158001400-158005800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:158001400-158005800	Weak transcription	HSMM	muscle
25	chr1:158001400-158006000	Weak transcription	Fetal Kidney	kidney
26	chr1:158001400-158006400	Weak transcription	Placenta	Placenta
27	chr1:158001400-158007400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:158001400-158007400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:158001400-158007400	Weak transcription	Aorta	Aorta
30	chr1:158001600-158007400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:158002000-158006400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:158002200-158006200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:158002200-158006400	Weak transcription	Fetal Intestine Small	intestine
34	chr1:158002400-158025400	Weak transcription	Fetal Brain Female	brain
35	chr1:158002600-158007400	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:158003400-158006600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:158003600-158006200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:158004200-158006000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:158004400-158006400	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr1:158004400-158006400	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr1:158004400-158006400	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr1:158004800-158006200	Enhancers	Osteobl	bone
43	chr1:158004800-158007400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:158004800-158009400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr1:158005000-158006400	Enhancers	NHDF-Ad	bronchial
46	chr1:158005000-158006600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:158005000-158006600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:158005000-158006800	Genic enhancers	NHLF	lung
49	chr1:158005000-158007400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:158005000-158007400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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