Variant report

Variant	rs4148807
Chromosome Location	chr7:87105812-87105813
allele	C/T
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	chr7:87103555-87106431	GM12878	blood:	n/a	n/a
2	PML	chr7:87103192-87105843	GM12878	blood:	n/a	n/a
3	CHD1	chr7:87105625-87106080	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:87103275-87105942	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:87103429-87106200	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CROT-1	chr7:87105081-87107196	NONHSAT121834

Variant related genes	Relation type
ABCB4	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1055302	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11974333	0.93[ASN][1000 genomes]
rs12538707	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12539936	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs12539997	0.92[ASN][1000 genomes]
rs12672720	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12673662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1468615	0.80[AMR][1000 genomes]
rs17149637	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17149640	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17149641	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17149647	1.00[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs17149652	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17149660	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17209662	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17209837	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17275514	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2072383	1.00[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2302385	1.00[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs2302386	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2302387	1.00[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs31672	0.91[CEU][hapmap]
rs3842	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4148805	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4148808	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4148814	1.00[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4148815	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4148817	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4148822	0.81[GIH][hapmap]
rs45447097	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs45478299	0.96[ASN][1000 genomes]
rs45496691	0.96[ASN][1000 genomes]
rs45502492	0.99[EUR][1000 genomes]
rs45526438	0.99[EUR][1000 genomes]
rs45537841	0.96[ASN][1000 genomes]
rs45546132	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs45554032	0.97[EUR][1000 genomes]
rs45560338	0.96[ASN][1000 genomes]
rs45590633	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs45593435	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs45605032	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs45607141	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55747905	0.92[ASN][1000 genomes]
rs56223611	0.98[EUR][1000 genomes]
rs60123540	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60541816	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60916103	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6465116	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs66510518	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67721532	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73198345	0.95[ASN][1000 genomes]
rs7782643	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7789645	0.92[ASN][1000 genomes]
rs7793196	0.92[ASN][1000 genomes]
rs7802555	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7802783	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs998671	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	53 gene(s)	inside rSNPs	diseases
5	nsv464622	chr7:86832603-87541248	Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv607725	chr7:86832603-87541248	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv1029486	chr7:86856387-87121976	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv539004	chr7:86856387-87121976	Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	esv1828294	chr7:86857553-87147397	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv1024376	chr7:86905796-87129346	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv1026153	chr7:86905796-87258822	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	esv3382480	chr7:87031452-87133648	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv464623	chr7:87040629-87139316	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv607726	chr7:87040629-87139316	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	esv1792643	chr7:87069758-87108420	Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv1015862	chr7:87075394-88049798	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
17	nsv888689	chr7:87093247-87110017	Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv888690	chr7:87093247-87122847	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	esv3346922	chr7:87103841-87106389	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4148807	FZD1	cis	parietal	SCAN
rs4148807	ABCB4	Cis_1M	lymphoblastoid	RTeQTL
rs4148807	ABCB1///ABCB4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:87104800-87108000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr7:87105400-87106000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr7:87105600-87106000	Active TSS	GM12878-XiMat	blood
4	chr7:87105600-87107000	Enhancers	HepG2	liver
5	chr7:87105800-87106000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
6	chr7:87105800-87106200	Enhancers	Primary B cells from cord blood	blood
7	chr7:87105800-87106800	Enhancers	Primary B cells from peripheral blood	blood
8	chr7:87105800-87108200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:87105800-87108600	Weak transcription	Liver	Liver

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