Variant report

No.	Distal block	Cell Line	Cell type
1	chr6:37604239..37606092-chr6:37613007..37615064,2	K562	blood:
2	chr6:37599758..37602608-chr6:37603760..37606026,2	MCF-7	breast:
3	chr6:37601797..37603781-chr6:37603910..37605765,2	K562	blood:
4	chr6:37603854..37605395-chr6:37609156..37610815,2	K562	blood:
5	chr6:37590338..37593047-chr6:37604192..37605778,2	K562	blood:
6	chr6:37600269..37601782-chr6:37603463..37605796,2	K562	blood:
7	chr6:37601453..37608472-chr6:37609186..37615415,9	K562	blood:

Variant related genes	Relation type
ENSG00000112139	Chromatin interaction

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10947686	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12191285	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191311	0.82[TSI][hapmap]
rs4714087	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs708023	0.91[ASN][1000 genomes]
rs7748104	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804839	0.97[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	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7748388	MDGA1	cis	Esophagus Mucosa	GTEx
rs7748388	MDGA1	cis	Skin Sun Exposed Lower leg	GTEx
rs7748388	TBC1D22B	cis	cerebellum	SCAN
rs7748388	GLP1R	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37594000-37615400	Weak transcription	Fetal Brain Female	brain
2	chr6:37598800-37606400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:37598800-37606600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:37599000-37605800	Weak transcription	A549	lung
5	chr6:37599200-37615600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:37599200-37621800	Weak transcription	NHLF	lung
7	chr6:37600400-37611400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr6:37602200-37616600	Weak transcription	Right Atrium	heart
9	chr6:37602600-37610000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:37602800-37605800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:37602800-37616400	Weak transcription	Ovary	ovary
12	chr6:37603000-37605200	Enhancers	Fetal Muscle Leg	muscle
13	chr6:37603400-37605000	Enhancers	Fetal Muscle Trunk	muscle
14	chr6:37603600-37605000	Enhancers	Hela-S3	cervix
15	chr6:37603800-37604800	Enhancers	Duodenum Mucosa	Duodenum
16	chr6:37603800-37605400	Enhancers	Spleen	Spleen
17	chr6:37604000-37605400	Enhancers	Esophagus	oesophagus
18	chr6:37604000-37610000	Weak transcription	Fetal Brain Male	brain
19	chr6:37604000-37611800	Weak transcription	Brain Germinal Matrix	brain
20	chr6:37604200-37614600	Strong transcription	Fetal Stomach	stomach
21	chr6:37604400-37611600	Weak transcription	Small Intestine	intestine

Quick Search: