Variant report

Variant	rs12679960
Chromosome Location	chr8:11430990-11430991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr8:11430934-11431188	HepG2	liver:	n/a	n/a
2	MAFK	chr8:11430931-11431204	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:11422187..11423813-chr8:11429710..11432078,2	MCF-7	breast:
2	chr8:11429172..11431915-chr8:11433216..11435875,2	MCF-7	breast:
3	chr8:11429899..11432844-chr8:11444265..11445875,2	MCF-7	breast:
4	chr8:11430263..11432062-chr8:11433287..11435276,2	K562	blood:

Variant related genes	Relation type
LINC00208	TF binding region
ENSG00000170983	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12547947	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2127128	1.00[CHB][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35353728	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35401006	0.80[AMR][1000 genomes]
rs4841557	0.81[AMR][1000 genomes]
rs4841558	0.81[AMR][1000 genomes]
rs4841566	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6988443	0.82[AMR][1000 genomes]
rs7007439	1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs7011778	1.00[JPT][hapmap];0.83[MEX][hapmap]
rs7834638	1.00[JPT][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes]
rs7840433	1.00[JPT][hapmap]
rs899366	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968179	0.86[CEU][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv34097	chr8:11177372-11489894	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1017865	chr8:11377795-11579954	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1026837	chr8:11394466-11464127	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1018959	chr8:11395232-11455756	Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv890358	chr8:11396856-11448738	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1033629	chr8:11401789-11466745	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv523827	chr8:11408401-11486220	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1032195	chr8:11420541-11480692	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1016749	chr8:11422571-11466745	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12679960	CLDN23	cis	multi-tissue	Pritchard
rs12679960	C8orf13	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11425200-11440400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:11427400-11431000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr8:11428400-11431000	Enhancers	Left Ventricle	heart
4	chr8:11428400-11431200	Enhancers	Placenta	Placenta
5	chr8:11428800-11431000	Enhancers	Right Ventricle	heart
6	chr8:11429000-11431000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr8:11429000-11431000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr8:11429000-11431000	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr8:11429000-11431000	Enhancers	Pancreas	Pancrea
10	chr8:11429000-11431600	Enhancers	Ovary	ovary
11	chr8:11429200-11431000	Enhancers	Gastric	stomach
12	chr8:11429200-11431000	Enhancers	Spleen	Spleen
13	chr8:11429200-11431400	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr8:11429200-11432600	Enhancers	Stomach Mucosa	stomach
15	chr8:11429400-11431000	Enhancers	Esophagus	oesophagus
16	chr8:11429600-11431000	Enhancers	Right Atrium	heart
17	chr8:11429600-11431600	Enhancers	HepG2	liver
18	chr8:11429800-11431000	Enhancers	Psoas Muscle	Psoas
19	chr8:11430200-11431600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
20	chr8:11430400-11431000	Enhancers	Duodenum Mucosa	Duodenum
21	chr8:11430400-11431400	Bivalent Enhancer	Hela-S3	cervix
22	chr8:11430600-11431000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
23	chr8:11430800-11431000	Flanking Active TSS	Fetal Heart	heart
24	chr8:11430800-11431000	Bivalent Enhancer	Fetal Stomach	stomach
25	chr8:11430800-11431000	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr8:11430800-11431400	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
27	chr8:11430800-11431600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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