Variant report

Variant	rs4604289
Chromosome Location	chr6:140296625-140296626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:139696942..139698780-chr6:140294038..140296688,2	K562	blood:
2	chr6:139697609..139700104-chr6:140295382..140298304,2	MCF-7	breast:
3	chr6:139693589..139696606-chr6:140296332..140298975,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1028467	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12197784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12202967	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1338692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1977739	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2211064	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328001	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4416686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570387	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6906538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7751424	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9495615	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9495620	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140287800-140299000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:140289600-140297200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:140291600-140302000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:140292600-140297000	Weak transcription	Placenta	Placenta
5	chr6:140292600-140306000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:140294200-140299400	Enhancers	Fetal Heart	heart
7	chr6:140295200-140299000	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:140295200-140303000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr6:140295400-140297000	Weak transcription	NHDF-Ad	bronchial
10	chr6:140295400-140297600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:140295400-140298000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:140295400-140298600	Weak transcription	A549	lung
13	chr6:140295400-140298800	Weak transcription	HSMMtube	muscle
14	chr6:140295400-140300400	Weak transcription	Fetal Kidney	kidney
15	chr6:140295400-140300400	Weak transcription	Fetal Stomach	stomach
16	chr6:140295400-140300400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:140295400-140301800	Weak transcription	Aorta	Aorta
18	chr6:140295400-140302000	Weak transcription	Adipose Nuclei	Adipose
19	chr6:140295400-140302800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:140295400-140303000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:140295600-140297400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:140295600-140298200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:140295600-140298600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:140295600-140298800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:140295600-140299000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:140295600-140302000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:140295600-140302600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:140295600-140303400	Weak transcription	Right Atrium	heart
29	chr6:140295800-140298600	Weak transcription	HSMM	muscle
30	chr6:140295800-140298800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:140295800-140298800	Weak transcription	NH-A	brain
32	chr6:140295800-140299000	Weak transcription	HUVEC	blood vessel
33	chr6:140295800-140299000	Weak transcription	K562	blood
34	chr6:140296000-140297200	Enhancers	NHLF	lung
35	chr6:140296000-140298200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:140296400-140298200	Weak transcription	Hela-S3	cervix
37	chr6:140296400-140298800	Weak transcription	Osteobl	bone
38	chr6:140296400-140302600	Weak transcription	Fetal Lung	lung
39	chr6:140296600-140296800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:140296600-140296800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:140296600-140298200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:140296600-140298200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr6:140296600-140298400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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