Variant report

Variant	rs4719260
Chromosome Location	chr7:11203796-11203797
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:11196790..11199292-chr7:11202946..11205439,2	K562	blood:
2	chr7:11196790..11199546-chr7:11202946..11205522,2	K562	blood:

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10234395	0.85[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10236024	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs10245045	0.92[CEU][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs10246100	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10251095	0.83[CHB][hapmap]
rs10251185	0.84[CHB][hapmap]
rs10255688	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs1057436	0.84[CHB][hapmap]
rs1154922	0.84[CHB][hapmap]
rs11560245	0.84[CHB][hapmap]
rs11978518	0.84[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap]
rs12112674	0.84[CHB][hapmap]
rs12699172	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs13222039	0.95[ASN][1000 genomes]
rs13238887	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs13241511	0.84[CHB][hapmap]
rs1483201	0.84[CHB][hapmap]
rs1483203	0.82[CHB][hapmap]
rs1547945	0.83[CHB][hapmap]
rs1640700	0.83[CHB][hapmap]
rs1681291	0.86[JPT][hapmap]
rs1681302	0.84[CHB][hapmap]
rs1681305	0.84[CHB][hapmap]
rs1681310	0.83[CHB][hapmap]
rs2108111	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs2214858	0.84[CHB][hapmap];0.82[CHD][hapmap];0.82[MEX][hapmap]
rs2353791	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2906543	0.84[CHB][hapmap]
rs2906544	0.84[CHB][hapmap]
rs2906545	0.84[CHB][hapmap]
rs2906548	0.84[CHB][hapmap]
rs2906550	0.81[CHB][hapmap]
rs2906551	0.83[CHB][hapmap]
rs2906552	0.84[CHB][hapmap]
rs2906553	0.84[CHB][hapmap];0.82[MEX][hapmap]
rs2906555	0.84[CHB][hapmap]
rs2906556	0.92[CHB][hapmap]
rs2906560	0.84[CHB][hapmap]
rs2906565	0.84[CHB][hapmap]
rs2995878	0.84[CHB][hapmap]
rs2995879	0.84[CHB][hapmap]
rs2995880	0.84[CHB][hapmap]
rs2995881	0.84[CHB][hapmap]
rs2995884	0.91[CHB][hapmap]
rs2995898	0.84[CHB][hapmap]
rs2995903	0.84[CHB][hapmap]
rs3801437	0.84[CHB][hapmap]
rs3801453	0.84[CHB][hapmap]
rs3823875	0.84[CHB][hapmap]
rs4314555	0.84[CHB][hapmap]
rs4644135	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs4719258	0.84[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap]
rs4720938	0.84[CHB][hapmap];0.82[CHD][hapmap];0.82[MEX][hapmap]
rs4720944	0.89[ASN][1000 genomes]
rs4720945	0.81[GIH][hapmap]
rs4720946	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[ASN][1000 genomes]
rs6460785	0.84[CHB][hapmap]
rs6460789	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6460790	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6944741	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6951444	0.81[GIH][hapmap]
rs6953287	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6953496	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6954805	0.83[CHB][hapmap];0.82[CHD][hapmap];0.81[MEX][hapmap]
rs6957940	0.84[CHB][hapmap]
rs6966809	0.89[ASN][1000 genomes]
rs7785008	0.84[CHB][hapmap];0.86[CHD][hapmap];0.82[MEX][hapmap]
rs7786922	0.84[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7790383	0.84[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap]
rs7791995	0.84[CHB][hapmap]
rs7798427	0.92[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7806840	0.81[CHB][hapmap]
rs7810754	0.80[CEU][hapmap]
rs9638668	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9986755	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067780	chr7:10649696-11329787	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv491695	chr7:10649696-11329787	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1019888	chr7:10712858-11496785	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1029836	chr7:10713523-11492751	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
5	nsv538730	chr7:10713523-11492751	Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv532092	chr7:10731350-11414759	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer 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
7	nsv1024171	chr7:10810444-11559156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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	nsv949387	chr7:10815994-11281536	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv1029882	chr7:10872162-11371145	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv817291	chr7:10875417-11562683	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv1030035	chr7:11027819-11256089	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
12	nsv887602	chr7:11071993-11220846	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
13	nsv428162	chr7:11085784-11359333	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
14	nsv830901	chr7:11093455-11272219	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv887603	chr7:11104985-11231727	Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
16	nsv606195	chr7:11140383-11216782	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
17	nsv606196	chr7:11144030-11255948	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
18	nsv1029654	chr7:11147593-11263834	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
19	nsv538731	chr7:11147593-11263834	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
20	nsv523279	chr7:11198193-11473561	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	nsv518180	chr7:11198193-11475819	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4719260	NXPH1	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:11107600-11212200	Weak transcription	Fetal Kidney	kidney
2	chr7:11113200-11211800	Weak transcription	Fetal Intestine Large	intestine
3	chr7:11114600-11210000	Weak transcription	Fetal Brain Female	brain
4	chr7:11156400-11209800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr7:11168200-11208800	Weak transcription	Primary T cells from cord blood	blood
6	chr7:11169000-11208800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:11170600-11217400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:11175400-11206000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr7:11175400-11213200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:11180000-11210400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:11183600-11208800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:11188200-11208400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:11189000-11210400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:11189200-11214000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:11190000-11213200	Weak transcription	Dnd41	blood
16	chr7:11193200-11211200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:11195400-11210000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:11198200-11209600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr7:11199800-11210200	Weak transcription	Fetal Lung	lung
20	chr7:11200200-11208400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:11200600-11205800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr7:11203200-11204200	Strong transcription	Primary B cells from cord blood	blood
23	chr7:11203600-11203800	Enhancers	Pancreatic Islets	Pancreatic Islet

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