Variant report

Variant	rs12699131
Chromosome Location	chr7:71751316-71751317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10215010	0.93[ASN][1000 genomes]
rs10215011	0.92[ASN][1000 genomes]
rs10215139	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10215553	0.93[ASN][1000 genomes]
rs10216201	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10231072	0.85[ASN][1000 genomes]
rs10234843	0.94[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10234985	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10238714	0.94[ASN][1000 genomes]
rs10238909	0.94[ASN][1000 genomes]
rs10239699	0.94[ASN][1000 genomes]
rs10243625	0.99[ASN][1000 genomes]
rs10243740	0.94[ASN][1000 genomes]
rs10244985	0.97[ASN][1000 genomes]
rs10253092	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10256008	0.86[ASN][1000 genomes]
rs10256020	0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10268103	0.97[ASN][1000 genomes]
rs1034618	0.94[ASN][1000 genomes]
rs1034619	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10464195	0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10950305	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs11766229	0.87[ASN][1000 genomes]
rs11767480	0.92[ASN][1000 genomes]
rs11767481	0.91[ASN][1000 genomes]
rs11770522	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11971387	0.85[ASN][1000 genomes]
rs11981552	0.96[ASN][1000 genomes]
rs11983557	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12532494	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12667297	0.83[CHB][hapmap]
rs12670234	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13242763	0.85[ASN][1000 genomes]
rs13244117	0.90[CHB][hapmap]
rs13247007	0.81[CHB][hapmap]
rs13247156	0.83[CHB][hapmap]
rs16869625	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1914384	0.94[ASN][1000 genomes]
rs1914385	0.96[ASN][1000 genomes]
rs1914386	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1914390	0.94[ASN][1000 genomes]
rs1914398	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1914399	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1978102	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2677275	0.83[CHB][hapmap]
rs28401746	0.92[ASN][1000 genomes]
rs28432195	0.94[ASN][1000 genomes]
rs28441039	0.82[ASN][1000 genomes]
rs28531896	0.85[ASN][1000 genomes]
rs28548784	0.94[ASN][1000 genomes]
rs28605994	0.81[ASN][1000 genomes]
rs2867673	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28719656	0.97[ASN][1000 genomes]
rs28785225	0.93[ASN][1000 genomes]
rs2944833	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2944834	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2944839	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2968527	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs35058779	0.94[ASN][1000 genomes]
rs35417702	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35526560	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4317470	0.90[ASN][1000 genomes]
rs4512281	0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4517001	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4639398	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4645475	0.85[ASN][1000 genomes]
rs477387	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs485865	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs501383	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs548405	0.83[CHB][hapmap]
rs56150095	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs573092	0.83[CHB][hapmap]
rs59378249	0.87[ASN][1000 genomes]
rs61288133	0.94[ASN][1000 genomes]
rs61522141	0.87[ASN][1000 genomes]
rs6460711	0.99[ASN][1000 genomes]
rs6968408	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs6979866	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73704335	0.92[ASN][1000 genomes]
rs73704336	0.94[ASN][1000 genomes]
rs756912	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7782391	1.00[ASN][1000 genomes]
rs7782517	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531372	chr7:71300090-71909517	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv491610	chr7:71422560-71803630	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv531373	chr7:71487076-71765613	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv817506	chr7:71488542-71935721	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1034282	chr7:71531113-71876617	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv529620	chr7:71604785-71935721	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv492243	chr7:71648955-71935721	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1019700	chr7:71677836-71844973	Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv538943	chr7:71677836-71844973	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv607460	chr7:71713735-71817899	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1033860	chr7:71715105-71778772	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv538944	chr7:71715105-71778772	Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1032591	chr7:71715105-71794258	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv538945	chr7:71715105-71794258	Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv470299	chr7:71740458-71815170	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv464556	chr7:71740458-71817899	Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv464557	chr7:71744896-71935721	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv607461	chr7:71744896-71935721	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv1029656	chr7:71745055-71935721	Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	esv3477337	chr7:71750984-71753272	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	esv3477338	chr7:71750984-71753272	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
22	esv3518379	chr7:71751063-71753149	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
23	esv3518380	chr7:71751063-71753149	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	21926974	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12699131	CLDN3	cis	cerebellum	SCAN
rs12699131	HTT	trans	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:71732600-71760600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:71732800-71758000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:71750200-71752400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr7:71750200-71753400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr7:71750600-71751400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr7:71750600-71752400	Enhancers	Primary hematopoietic stem cells	blood
7	chr7:71750800-71751400	Enhancers	Thymus	Thymus
8	chr7:71750800-71752400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr7:71750800-71753200	Enhancers	Fetal Thymus	thymus
10	chr7:71751200-71752200	Enhancers	Adipose Nuclei	Adipose

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