Variant report

Variant	rs9257399
Chromosome Location	chr6:28916444-28916445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28915108..28916611-chr6:28956143..28957725,2	K562	blood:
2	chr6:28908842..28913919-chr6:28914065..28917198,6	K562	blood:
3	chr6:28916396..28919032-chr6:28931395..28932899,2	K562	blood:
4	chr6:28889181..28892324-chr6:28914059..28916550,3	MCF-7	breast:
5	chr6:28914281..28916611-chr6:28956056..28957643,2	K562	blood:
6	chr6:28830059..28832659-chr6:28914620..28916802,2	K562	blood:
7	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:

Variant related genes	Relation type
ENSG00000204709	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000263426	Chromatin interaction
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1061625	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1794588	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs209127	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2097424	0.81[ASN][1000 genomes]
rs2894066	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3130843	0.90[ASN][1000 genomes]
rs3131067	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3132377	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3132380	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6906953	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6912843	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6926892	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7740125	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs876737	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9257395	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9257412	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9257416	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9257424	0.84[ASN][1000 genomes]
rs9257425	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[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	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28912200-28921200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:28912400-28916800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:28912400-28920800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:28912400-28921200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:28912400-28921200	Weak transcription	Fetal Intestine Small	intestine
6	chr6:28912400-28921200	Weak transcription	Right Atrium	heart
7	chr6:28913200-28916600	Enhancers	K562	blood
8	chr6:28914400-28917000	Enhancers	Hela-S3	cervix
9	chr6:28915400-28916600	Enhancers	A549	lung
10	chr6:28915400-28916800	Flanking Active TSS	HepG2	liver
11	chr6:28915400-28917000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr6:28915400-28917000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:28915400-28917000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr6:28915600-28916600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr6:28915600-28921200	Weak transcription	Esophagus	oesophagus
16	chr6:28915800-28916600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:28915800-28916800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr6:28915800-28920600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:28916000-28917000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr6:28916000-28918400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:28916000-28918400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:28916000-28920800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:28916000-28921200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:28916200-28920800	Weak transcription	NH-A	brain
25	chr6:28916200-28920800	Weak transcription	Osteobl	bone
26	chr6:28916200-28921200	Weak transcription	HMEC	breast
27	chr6:28916200-28921200	Weak transcription	NHEK	skin
28	chr6:28916400-28921200	Weak transcription	Rectal Mucosa Donor 29	rectum

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