Variant report

Variant	rs13252797
Chromosome Location	chr8:8861430-8861431
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:8756284..8757870-chr8:8861137..8863458,2	K562	blood:
2	chr8:8860553..8862183-chr8:9011362..9013111,2	K562	blood:
3	chr8:8608069..8609942-chr8:8861282..8862933,2	MCF-7	breast:
4	chr8:8859472..8863506-chr8:8866779..8870820,4	MCF-7	breast:
5	chr8:8859158..8867027-chr8:8867199..8874373,17	K562	blood:

Variant related genes	Relation type
ENSG00000104626	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10087416	1.00[CHB][hapmap]
rs10217044	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1045527	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1045529	0.89[CEU][hapmap]
rs11784393	0.81[CEU][hapmap]
rs11785634	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11785819	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11787026	0.93[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs11990476	0.93[ASN][1000 genomes]
rs11992016	0.93[ASN][1000 genomes]
rs12114954	0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs12549151	0.81[ASN][1000 genomes]
rs13271797	1.00[CEU][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1562211	0.81[CEU][hapmap]
rs1594437	0.93[ASN][1000 genomes]
rs17702602	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs2043129	0.93[ASN][1000 genomes]
rs2043131	0.80[ASN][1000 genomes]
rs2060045	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2288671	0.85[CEU][hapmap]
rs2409120	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28482034	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28510464	1.00[ASN][1000 genomes]
rs28587518	0.93[ASN][1000 genomes]
rs28665409	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28740848	1.00[ASN][1000 genomes]
rs2915251	0.85[CEU][hapmap]
rs2956244	0.88[CEU][hapmap]
rs2979247	0.85[CEU][hapmap]
rs2979256	0.85[CEU][hapmap]
rs2979265	0.85[CEU][hapmap]
rs34004903	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34251783	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3827807	1.00[CHB][hapmap]
rs3855900	0.83[AMR][1000 genomes]
rs3895823	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4840381	0.86[ASN][1000 genomes]
rs4840389	0.88[EUR][1000 genomes]
rs4841083	0.92[CEU][hapmap]
rs57395675	0.93[ASN][1000 genomes]
rs57693332	0.87[ASN][1000 genomes]
rs58594457	0.93[ASN][1000 genomes]
rs59374911	0.93[ASN][1000 genomes]
rs59454995	0.86[ASN][1000 genomes]
rs60274012	0.93[ASN][1000 genomes]
rs62492946	0.81[ASN][1000 genomes]
rs6601279	0.81[AMR][1000 genomes]
rs6601280	0.92[CEU][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs6601281	0.82[AMR][1000 genomes]
rs6601282	0.81[CEU][hapmap]
rs6748	1.00[CEU][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6981060	0.81[AMR][1000 genomes]
rs6983877	0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs6986044	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6987107	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6987558	0.85[CEU][hapmap]
rs7004160	0.86[ASN][1000 genomes]
rs7005056	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7005133	0.81[CEU][hapmap]
rs7014430	0.93[ASN][1000 genomes]
rs7014604	0.93[ASN][1000 genomes]
rs7016240	0.93[ASN][1000 genomes]
rs7017868	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73514373	0.86[ASN][1000 genomes]
rs73518314	0.86[ASN][1000 genomes]
rs73518320	0.86[ASN][1000 genomes]
rs73522594	0.93[ASN][1000 genomes]
rs73662257	0.93[ASN][1000 genomes]
rs7462373	0.82[AMR][1000 genomes]
rs7813355	1.00[CHB][hapmap]
rs7814328	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7814828	0.87[ASN][1000 genomes]
rs7820324	1.00[CHB][hapmap]
rs7836156	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9329175	0.96[CEU][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9650616	1.00[CEU][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9987276	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv831229	chr8:8751523-8926235	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv610205	chr8:8799111-8891644	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	n/a
5	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13252797	CLDN23	cis	multi-tissue	Pritchard
rs13252797	RP11-62H7.2	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8859600-8861600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr8:8859600-8862000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr8:8859600-8862000	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr8:8859800-8861600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr8:8859800-8861600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr8:8859800-8861800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:8859800-8861800	Active TSS	Psoas Muscle	Psoas
8	chr8:8859800-8862000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr8:8859800-8862000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr8:8859800-8862000	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr8:8859800-8862000	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr8:8860000-8861600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr8:8860000-8861600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr8:8860000-8862000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr8:8860000-8863400	Active TSS	K562	blood
16	chr8:8860200-8861600	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr8:8860200-8861600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr8:8860200-8861600	Active TSS	HSMM	muscle
19	chr8:8860200-8862000	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr8:8860200-8862200	Active TSS	Hela-S3	cervix
21	chr8:8860400-8861800	Active TSS	Pancreas	Pancrea
22	chr8:8860600-8861600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr8:8860600-8861600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr8:8860600-8861800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr8:8860600-8862000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr8:8860800-8861600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr8:8860800-8861600	Flanking Active TSS	Liver	Liver
28	chr8:8860800-8861600	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr8:8860800-8861600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr8:8860800-8861800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr8:8860800-8861800	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr8:8860800-8861800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr8:8860800-8862000	Flanking Active TSS	HUVEC	blood vessel
34	chr8:8860800-8862200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr8:8861000-8861600	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr8:8861000-8861600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr8:8861000-8861600	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr8:8861000-8861600	Flanking Active TSS	Fetal Brain Male	brain
39	chr8:8861000-8861600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr8:8861000-8861600	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr8:8861000-8861800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr8:8861000-8861800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr8:8861000-8861800	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr8:8861000-8861800	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr8:8861000-8861800	Flanking Active TSS	Brain Germinal Matrix	brain
46	chr8:8861000-8861800	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr8:8861000-8861800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr8:8861000-8861800	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr8:8861000-8861800	Flanking Active TSS	Fetal Brain Female	brain
50	chr8:8861000-8861800	Flanking Active TSS	Fetal Lung	lung

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