Variant report

Variant	rs1874953
Chromosome Location	chr15:76236837-76236838
allele	C/G
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	POLR2A	chr15:76236395-76236972	HUVEC	blood vessel:	n/a	n/a
2	BCL3	chr15:76236159-76237297	A549	lung:	n/a	chr15:76236250-76236259
3	POLR2A	chr15:76235470-76237205	MCF-7	breast:	n/a	n/a
4	POLR2A	chr15:76236591-76236848	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr15:76235479-76237167	GM12891	blood:	n/a	n/a
6	POLR2A	chr15:76235602-76236983	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr15:76230003-76237266	K562	blood:	n/a	n/a
8	POLR2A	chr15:76236723-76236875	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr15:76236324-76237085	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr15:76236244-76236903	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr15:76236659-76236848	K562	blood:	n/a	n/a
12	POLR2A	chr15:76236012-76236972	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr15:76234833-76237053	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr15:76234064-76237226	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:76235183-76237215	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr15:76236570-76237203	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr15:76235402-76237148	HepG2	liver:	n/a	n/a
18	POLR2A	chr15:76235578-76237055	A549	lung:	n/a	n/a
19	POLR2A	chr15:76235406-76237031	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76235823..76238133-chr15:76240535..76242101,2	K562	blood:
2	chr15:76231213..76235489-chr15:76235646..76238510,7	K562	blood:

Variant related genes	Relation type
NRG4	TF binding region
ENSG00000169752	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10444856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10851884	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11072562	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11072566	1.00[ASW][hapmap];0.93[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11072567	0.90[EUR][1000 genomes]
rs11636251	0.96[CEU][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12437816	1.00[CEU][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12593806	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1976748	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2047866	0.81[EUR][1000 genomes]
rs2088599	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2201917	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28525382	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28550045	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28607641	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs335685	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4886466	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4886748	0.96[CEU][hapmap];0.83[GIH][hapmap];0.87[LWK][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886755	0.93[ASW][hapmap];0.96[CEU][hapmap];0.81[LWK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes]
rs7177266	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8027685	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1053717	chr15:76196674-76314542	Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1040053	chr15:76197988-76314542	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv904398	chr15:76220285-76359055	Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv569998	chr15:76232605-76550938	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1874953	NRG4	cis	cerebellum	SCAN
rs1874953	NRG4	cis	parietal	SCAN
rs1874953	UBE2Q2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76211400-76240200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr15:76217200-76252000	Weak transcription	Pancreas	Pancrea
3	chr15:76226600-76238600	Weak transcription	NHLF	lung
4	chr15:76228200-76239600	Weak transcription	Fetal Brain Female	brain
5	chr15:76230600-76238600	Weak transcription	Left Ventricle	heart
6	chr15:76230600-76239400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:76230600-76244400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:76230800-76238200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr15:76230800-76246400	Weak transcription	Hela-S3	cervix
10	chr15:76231000-76239000	Weak transcription	Fetal Brain Male	brain
11	chr15:76231400-76239400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:76232200-76238400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr15:76232200-76239400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:76232400-76239200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:76232800-76239400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:76236000-76237000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr15:76236000-76237000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:76236000-76237000	Enhancers	NHEK	skin
19	chr15:76236000-76237000	Enhancers	Osteobl	bone
20	chr15:76236000-76237400	Enhancers	HSMMtube	muscle
21	chr15:76236000-76238800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:76236200-76237000	Enhancers	NH-A	brain
23	chr15:76236200-76237800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:76236600-76238400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:76236800-76238200	Weak transcription	HMEC	breast
26	chr15:76236800-76238200	Weak transcription	HSMM	muscle
27	chr15:76236800-76238400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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