Variant report

Variant	rs936524
Chromosome Location	chr19:39233146-39233147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39227434..39229644-chr19:39233125..39236145,3	MCF-7	breast:
2	chr19:39228306..39230279-chr19:39233041..39234658,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267892	Chromatin interaction
ENSG00000182472	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1031849	0.81[YRI][hapmap];0.87[AMR][1000 genomes]
rs10421863	0.86[CHB][hapmap];0.92[CHD][hapmap];0.95[MEX][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10424568	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs1060186	0.94[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11083476	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11665964	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11672576	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12462503	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs12984247	0.94[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs1564203	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2080988	0.90[AMR][1000 genomes]
rs2112649	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs3786841	0.90[AMR][1000 genomes]
rs3786843	0.88[AMR][1000 genomes]
rs4347742	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4619518	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4801861	0.94[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs4802743	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs4802797	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57845235	0.82[AMR][1000 genomes]
rs6508813	0.94[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap]
rs6508814	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7249585	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7252630	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs749701	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs752067	0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs8099948	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8107877	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs888997	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs9304576	0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs9304577	0.94[JPT][hapmap]

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	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs936524	CTD-2540F13.2	cis	Nerve Tibial	GTEx
rs936524	C19orf54	cis	parietal	SCAN
rs936524	CAPN12	cis	lymphoblastoid	seeQTL
rs936524	CAPN12	cis	Heart Left Ventricle	GTEx
rs936524	CAPN12	cis	Adipose Subcutaneous	GTEx
rs936524	RPS16	cis	parietal	SCAN
rs936524	SFRS16	cis	parietal	SCAN
rs936524	MEGF8	cis	cerebellum	SCAN
rs936524	ERF	cis	cerebellum	SCAN
rs936524	CAPN12	cis	Esophagus Muscularis	GTEx
rs936524	LGALS17A	cis	cerebellum	SCAN
rs936524	CAPN12	cis	multi-tissue	Pritchard
rs936524	PPP1R13L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39227400-39234600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:39228400-39234600	Weak transcription	Placenta	Placenta
3	chr19:39228600-39234400	Weak transcription	A549	lung
4	chr19:39228800-39233800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:39229800-39233800	Weak transcription	Fetal Intestine Small	intestine
6	chr19:39230800-39234400	Weak transcription	K562	blood
7	chr19:39231000-39234400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr19:39231000-39234400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr19:39231000-39234600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:39232400-39233200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr19:39232400-39234400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:39232600-39234200	Weak transcription	Spleen	Spleen
13	chr19:39233000-39235200	Enhancers	HepG2	liver

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