Variant report

Variant	rs6665898
Chromosome Location	chr1:158003335-158003336
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	chr1:157998908..158001801-chr1:158002681..158007266,4	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10430456	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11264878	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12025305	0.98[ASN][1000 genomes]
rs12118340	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12118455	0.98[ASN][1000 genomes]
rs12134949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12568166	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16839617	0.81[JPT][hapmap]
rs16839627	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16839630	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16839636	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1925038	0.82[CEU][hapmap];0.94[YRI][hapmap]
rs1972216	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1980765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4445460	1.00[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs4971174	0.85[CEU][hapmap];0.97[YRI][hapmap]
rs4971177	0.82[CEU][hapmap];0.93[YRI][hapmap]
rs4971179	1.00[CEU][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4971180	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4971181	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971182	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971183	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971184	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971185	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs5018263	1.00[CEU][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs6661149	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6661160	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6664509	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6665788	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666443	0.85[CEU][hapmap];0.94[YRI][hapmap]
rs6680191	0.85[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6690504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6692314	0.98[ASN][1000 genomes]
rs6699860	0.96[ASN][1000 genomes]
rs7537784	0.82[CEU][hapmap]
rs7548850	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]

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:78 , 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	chr1:157995200-158004200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:157995400-158007600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:157995600-158004400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:157995800-158005600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:157995800-158007400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr1:157996000-158007400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:157996000-158007400	Weak transcription	Lung	lung
15	chr1:157996200-158006800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:157996200-158007600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:157996200-158007600	Weak transcription	Spleen	Spleen
18	chr1:157996400-158005600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:157996400-158007400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:157997200-158005600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr1:157997600-158004800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:157997600-158047600	Weak transcription	Dnd41	blood
23	chr1:157998000-158007400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:157998200-158007600	Weak transcription	Left Ventricle	heart
25	chr1:157999000-158006200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:157999000-158013000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:157999200-158005000	Weak transcription	Ovary	ovary
28	chr1:157999400-158005400	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:157999400-158005400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:158000200-158004000	Strong transcription	Fetal Stomach	stomach
31	chr1:158000200-158004400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:158000800-158003600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:158001000-158005000	Weak transcription	Fetal Lung	lung
34	chr1:158001200-158005000	Weak transcription	NHDF-Ad	bronchial
35	chr1:158001200-158011800	Weak transcription	Fetal Intestine Large	intestine
36	chr1:158001200-158047400	Weak transcription	Thymus	Thymus
37	chr1:158001400-158003600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:158001400-158004400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:158001400-158004400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:158001400-158005000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:158001400-158005600	Weak transcription	NH-A	brain
42	chr1:158001400-158005800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:158001400-158005800	Weak transcription	HSMM	muscle
44	chr1:158001400-158006000	Weak transcription	Fetal Kidney	kidney
45	chr1:158001400-158006400	Weak transcription	Placenta	Placenta
46	chr1:158001400-158007400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:158001400-158007400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:158001400-158007400	Weak transcription	Aorta	Aorta
49	chr1:158001600-158004400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:158001600-158005400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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