Variant report

Variant	rs197472
Chromosome Location	chr6:143076248-143076249
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	chr6:143072743..143074672-chr6:143075733..143079095,3	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs169098	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs197460	0.97[EUR][1000 genomes]
rs197462	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs197464	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs197475	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs197477	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs197482	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3383	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830828	chr6:142970134-143116517	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143059400-143080600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:143066200-143079000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr6:143067600-143080600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:143068200-143077400	Weak transcription	Fetal Lung	lung
5	chr6:143068200-143079600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:143071600-143080600	Weak transcription	Colonic Mucosa	Colon
7	chr6:143072200-143080600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:143072400-143077400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:143072400-143080600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:143072800-143077000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:143072800-143077800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:143072800-143078000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:143072800-143079400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr6:143072800-143080600	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:143072800-143094800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr6:143072800-143095200	Strong transcription	Fetal Thymus	thymus
17	chr6:143072800-143095400	Weak transcription	Fetal Kidney	kidney
18	chr6:143073000-143077000	Weak transcription	Fetal Heart	heart
19	chr6:143073000-143080400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:143073000-143083800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:143073000-143090800	Weak transcription	Right Atrium	heart
22	chr6:143073000-143096000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:143073200-143078000	Weak transcription	Fetal Brain Male	brain
24	chr6:143073600-143086400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:143073800-143077000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:143073800-143077800	Weak transcription	Hela-S3	cervix
27	chr6:143074000-143077000	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr6:143074000-143086600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:143074000-143086800	Strong transcription	Adipose Nuclei	Adipose
30	chr6:143074000-143094000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr6:143074200-143077000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:143074200-143077000	Strong transcription	Primary hematopoietic stem cells	blood
33	chr6:143074200-143077400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr6:143074200-143080800	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:143074200-143083000	Strong transcription	GM12878-XiMat	blood
36	chr6:143074600-143079600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:143074800-143076600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr6:143074800-143077200	Weak transcription	NH-A	brain
39	chr6:143074800-143077200	Weak transcription	NHDF-Ad	bronchial
40	chr6:143074800-143079200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:143074800-143080000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr6:143074800-143095800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:143075000-143076400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr6:143075000-143076400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:143075000-143076800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:143075000-143077000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:143075000-143077000	Weak transcription	HMEC	breast
48	chr6:143075000-143077200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:143075000-143077200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr6:143075000-143077200	Weak transcription	Osteobl	bone

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