Variant report

Variant	rs6699769
Chromosome Location	chr1:78504264-78504265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78504244..78506502-chr1:78511458..78513516,2	MCF-7	breast:
2	chr1:78500187..78503737-chr1:78504234..78506464,4	K562	blood:
3	chr1:8938682..8939404-chr1:78503985..78504778,2	Hela-S3	cervix:
4	chr1:78466509..78474870-chr1:78497253..78506543,20	K562	blood:
5	chr1:78477115..78479599-chr1:78501919..78504356,3	K562	blood:
6	chr1:78490302..78495506-chr1:78500007..78505511,6	K562	blood:

Variant related genes	Relation type
ENSG00000137960	Chromatin interaction
ENSG00000273338	Chromatin interaction
ENSG00000074800	Chromatin interaction
ENSG00000162616	Chromatin interaction
ENSG00000230679	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11162404	0.84[YRI][hapmap]
rs11162408	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1166698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs12067638	0.92[MKK][hapmap]
rs12086102	0.84[YRI][hapmap]
rs28735417	0.83[ASW][hapmap];0.85[CHB][hapmap]
rs614836	0.81[CEU][hapmap]
rs640935	1.00[YRI][hapmap]
rs6424659	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6669039	0.92[MKK][hapmap]
rs6702939	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7514180	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7537908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9726525	0.86[CHB][hapmap];0.90[JPT][hapmap]

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	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6699769	NEXN	Cis_1M	lymphoblastoid	RTeQTL
rs6699769	NEXN	cis	lymphoblastoid	seeQTL
rs6699769	DNAJB4	Cis_1M	lymphoblastoid	RTeQTL
rs6699769	NEXN	cis	multi-tissue	Pritchard
rs6699769	DNAJB4	cis	parietal	SCAN
rs6699769	TYW3	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78486400-78509400	Weak transcription	HSMM	muscle
2	chr1:78499400-78509200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:78499600-78505000	Weak transcription	Pancreas	Pancrea
4	chr1:78499600-78509200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:78500200-78506600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:78503400-78505200	Enhancers	HUVEC	blood vessel
7	chr1:78503600-78504400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr1:78503600-78504400	Enhancers	Hela-S3	cervix
9	chr1:78503800-78504400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:78503800-78504400	Enhancers	Colon Smooth Muscle	Colon
11	chr1:78503800-78504400	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr1:78503800-78504400	Enhancers	Fetal Lung	lung
13	chr1:78503800-78504400	Enhancers	Rectal Smooth Muscle	rectum
14	chr1:78503800-78504600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:78503800-78505000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:78503800-78505200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:78504000-78504400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:78504000-78506200	Weak transcription	Ovary	ovary
19	chr1:78504000-78510400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:78504200-78504400	Enhancers	NH-A	brain
21	chr1:78504200-78509200	Weak transcription	NHLF	lung
22	chr1:78504200-78509400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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