Variant report

Variant	rs1830068
Chromosome Location	chr7:16850389-16850390
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:16832553..16834809-chr7:16849103..16850683,2	MCF-7	breast:
2	chr7:16839844..16843226-chr7:16849835..16853685,4	MCF-7	breast:
3	chr7:16847748..16852819-chr7:16884544..16888713,8	MCF-7	breast:
4	chr7:16849977..16852539-chr7:16919446..16921847,2	MCF-7	breast:
5	chr7:16850191..16850816-chr7:16919955..16920542,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173467	Chromatin interaction
ENSG00000106541	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10085386	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10253218	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10263864	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10264144	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10266810	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10275787	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1149528	0.87[CEU][hapmap];0.92[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1149529	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1149530	0.83[AMR][1000 genomes]
rs12154501	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12699808	0.81[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12699812	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1357993	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1380384	0.84[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1404965	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1404970	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1404972	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1474413	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1563782	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1608878	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4721543	0.96[EUR][1000 genomes]
rs6461279	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6970631	0.93[CEU][hapmap];0.91[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs706070	0.90[MEX][hapmap];0.85[TSI][hapmap]
rs706071	0.92[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs706072	1.00[ASW][hapmap];0.93[CEU][hapmap];0.92[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs706074	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7776631	0.84[CHB][hapmap]
rs7780106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7783269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7791790	0.93[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7796749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7803549	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807024	0.93[CEU][hapmap];0.84[CHB][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs818800	0.80[CEU][hapmap];0.81[AMR][1000 genomes]
rs819007	1.00[ASW][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887761	chr7:16834361-17732490	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv887762	chr7:16834361-17746628	Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv887763	chr7:16834361-17750811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv887764	chr7:16839835-17218800	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv887765	chr7:16839835-17750811	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1027284	chr7:16849986-17008167	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1830068	AGR2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16844600-16854800	Weak transcription	Small Intestine	intestine
2	chr7:16845400-16852200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr7:16845400-16852800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:16846200-16850400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr7:16848000-16858200	Enhancers	Stomach Mucosa	stomach
6	chr7:16848400-16850600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr7:16849400-16853400	Enhancers	Fetal Intestine Large	intestine
8	chr7:16849400-16853400	Enhancers	Fetal Intestine Small	intestine
9	chr7:16849400-16857600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr7:16849600-16852200	Flanking Active TSS	A549	lung
11	chr7:16850200-16850600	Enhancers	Hela-S3	cervix
12	chr7:16850200-16851400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr7:16850200-16851600	Active TSS	Rectal Mucosa Donor 29	rectum

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