Variant report

Variant	rs6938489
Chromosome Location	chr6:45574839-45574840
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:45387446..45391966-chr6:45573986..45578620,7	MCF-7	breast:
2	chr6:45472331..45474237-chr6:45572643..45575608,3	MCF-7	breast:
3	chr6:45565614..45568174-chr6:45573417..45574937,2	K562	blood:
4	chr6:45502609..45505382-chr6:45574520..45576120,2	MCF-7	breast:
5	chr6:45387362..45392710-chr6:45572193..45578571,10	MCF-7	breast:
6	chr6:45573666..45576304-chr6:45593015..45594569,2	K562	blood:
7	chr6:45574169..45577727-chr6:45643786..45647502,3	MCF-7	breast:
8	chr6:45554176..45557433-chr6:45573679..45578604,5	MCF-7	breast:
9	chr20:52209163..52211952-chr6:45573690..45575433,2	MCF-7	breast:
10	chr6:45344957..45347513-chr6:45573194..45576058,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000271857	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000124813	Chromatin interaction
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12528502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661124	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12663210	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12665637	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1491142	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16873543	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16873550	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs16873554	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2020084	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56083876	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs57939401	0.85[ASN][1000 genomes]
rs58939587	0.85[ASN][1000 genomes]
rs59074904	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60540355	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6458449	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458450	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6458453	0.80[ASN][1000 genomes]
rs6458454	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6458455	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6899443	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6930188	0.82[ASN][1000 genomes]
rs6936365	0.80[ASN][1000 genomes]
rs6938247	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs6938758	0.81[AFR][1000 genomes]
rs713270	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73457129	0.92[AFR][1000 genomes]
rs73738526	0.80[ASN][1000 genomes]
rs7742335	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7752183	0.85[ASN][1000 genomes]
rs7752200	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7758915	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7759415	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7760394	0.84[AFR][1000 genomes]
rs7764338	0.85[YRI][hapmap];0.85[AFR][1000 genomes]
rs7766534	0.85[ASN][1000 genomes]
rs7768962	0.85[ASN][1000 genomes]
rs9296462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9296463	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9463108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9472518	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9472521	0.85[ASN][1000 genomes]
rs9472524	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9472525	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9472530	0.85[ASN][1000 genomes]
rs9472531	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs997445	0.83[CEU][hapmap]

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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45563800-45586200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:45564200-45579200	Weak transcription	Fetal Kidney	kidney
3	chr6:45571200-45575400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr6:45572800-45575400	Enhancers	Hela-S3	cervix
5	chr6:45573600-45577800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr6:45574200-45575400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:45574400-45578200	Enhancers	Dnd41	blood
8	chr6:45574400-45579600	Enhancers	Stomach Mucosa	stomach
9	chr6:45574600-45576600	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr6:45574600-45577400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:45574600-45577600	Enhancers	HMEC	breast
12	chr6:45574600-45578000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:45574800-45575000	Enhancers	Duodenum Mucosa	Duodenum
14	chr6:45574800-45575200	Enhancers	Esophagus	oesophagus
15	chr6:45574800-45576200	Weak transcription	Small Intestine	intestine
16	chr6:45574800-45577000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:45574800-45579400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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