Variant report

Variant	rs11112421
Chromosome Location	chr12:105636578-105636579
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105624829..105626862-chr12:105636321..105638776,2	MCF-7	breast:
2	chr12:105636186..105637706-chr17:16342913..16345886,3	K562	blood:
3	chr12:105631933..105633893-chr12:105636355..105638544,2	K562	blood:
4	chr12:105627699..105634093-chr12:105635156..105638470,6	K562	blood:
5	chr12:105628928..105631591-chr12:105632421..105636831,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136044	Chromatin interaction
ENSG00000266651	Chromatin interaction
ENSG00000235162	Chromatin interaction
ENSG00000175061	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1014502	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10431460	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10459203	0.82[CEU][hapmap]
rs10459204	0.82[CEU][hapmap];1.00[MEX][hapmap]
rs1057110	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1077896	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10861334	0.80[CEU][hapmap]
rs10861339	0.81[CEU][hapmap]
rs10861359	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10861361	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10861363	0.84[CEU][hapmap];0.83[CHB][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10861367	0.82[AFR][1000 genomes]
rs1109433	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11112369	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11112370	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs11112372	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11112375	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11112376	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11112379	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11112388	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11112409	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11112412	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11112415	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11112416	1.00[CEU][hapmap];0.80[GIH][hapmap];0.86[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11112423	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112433	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11112440	0.82[AFR][1000 genomes]
rs11831854	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11832489	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11834277	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12228093	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12228948	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12580027	0.82[AFR][1000 genomes]
rs12812433	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12815031	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12819309	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819795	0.82[AFR][1000 genomes]
rs12823614	0.82[CEU][hapmap];1.00[MEX][hapmap]
rs12830078	0.80[EUR][1000 genomes]
rs1317955	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1373552	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1444611	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1470381	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2166143	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs2272495	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2293643	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2293644	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28549976	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34075890	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34983773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35462155	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35672903	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3736628	0.84[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3794222	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3794223	1.00[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3794224	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794227	0.94[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3817607	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3829296	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4964125	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964128	0.82[ASN][1000 genomes]
rs4964334	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4964335	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4964336	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4964338	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4964339	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4964340	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4964342	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4964347	0.81[ASN][1000 genomes]
rs4964351	0.82[AFR][1000 genomes]
rs4964352	0.82[AFR][1000 genomes]
rs4964353	0.83[CHB][hapmap]
rs55908437	0.81[EUR][1000 genomes]
rs56693261	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7132894	0.96[GIH][hapmap]
rs73179994	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7484699	0.81[ASN][1000 genomes]
rs7485364	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7485511	0.82[AFR][1000 genomes]
rs7485535	0.82[AFR][1000 genomes]
rs7487098	0.81[ASN][1000 genomes]
rs755604	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8015	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs881279	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9919746	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
4	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11112421	KIAA1033	cis	cerebellum	SCAN
rs11112421	C12orf75	cis	cerebellum	SCAN
rs11112421	TDG	cis	parietal	SCAN
rs11112421	APPL2	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105630800-105639000	Weak transcription	Pancreas	Pancrea
2	chr12:105630800-105639000	Weak transcription	NHLF	lung
3	chr12:105632400-105638800	Weak transcription	NHDF-Ad	bronchial
4	chr12:105633800-105637000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr12:105633800-105638800	Weak transcription	Osteobl	bone
6	chr12:105633800-105639000	Weak transcription	Gastric	stomach
7	chr12:105633800-105639200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:105636400-105637200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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