Variant report

Variant	rs7259404
Chromosome Location	chr19:45661501-45661502
allele	A/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	BCL3	chr19:45661187-45661595	A549	lung:	n/a	n/a
2	POLR2A	chr19:45661331-45661743	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr19:45661460-45661610	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:45661385-45661866	MCF-7	breast:	n/a	n/a
5	POLR2A	chr19:45661444-45663621	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:45576440..45580394-chr19:45659978..45661759,3	MCF-7	breast:
2	chr19:45658848..45663469-chr19:45680259..45684163,6	MCF-7	breast:

Variant related genes	Relation type
NKPD1	TF binding region
ENSG00000170684	Chromatin interaction
ENSG00000189114	Chromatin interaction
ENSG00000267545	Chromatin interaction
ENSG00000007255	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10402479	1.00[ASN][1000 genomes]
rs10403214	1.00[ASN][1000 genomes]
rs10405306	1.00[ASN][1000 genomes]
rs10405719	1.00[ASN][1000 genomes]
rs10405721	1.00[ASN][1000 genomes]
rs10406911	1.00[ASN][1000 genomes]
rs10408366	1.00[ASN][1000 genomes]
rs10408462	1.00[ASN][1000 genomes]
rs10409138	1.00[ASN][1000 genomes]
rs10409232	1.00[ASN][1000 genomes]
rs10409727	1.00[ASN][1000 genomes]
rs10409903	1.00[ASN][1000 genomes]
rs10410424	1.00[ASN][1000 genomes]
rs10415674	1.00[ASN][1000 genomes]
rs10417101	1.00[ASN][1000 genomes]
rs10417347	1.00[ASN][1000 genomes]
rs10417618	1.00[ASN][1000 genomes]
rs10417804	1.00[ASN][1000 genomes]
rs10419874	1.00[ASN][1000 genomes]
rs10420717	1.00[ASN][1000 genomes]
rs10420824	1.00[ASN][1000 genomes]
rs10421085	1.00[ASN][1000 genomes]
rs10421425	1.00[ASN][1000 genomes]
rs10421932	1.00[ASN][1000 genomes]
rs10422671	1.00[ASN][1000 genomes]
rs10423079	1.00[ASN][1000 genomes]
rs10423555	1.00[ASN][1000 genomes]
rs10424651	1.00[ASN][1000 genomes]
rs10425380	1.00[ASN][1000 genomes]
rs10425938	1.00[AMR][1000 genomes]
rs1076384	1.00[ASN][1000 genomes]
rs12459386	1.00[ASN][1000 genomes]
rs12459402	1.00[ASN][1000 genomes]
rs12459945	1.00[ASN][1000 genomes]
rs12461749	1.00[ASN][1000 genomes]
rs13344055	1.00[ASN][1000 genomes]
rs13344075	1.00[ASN][1000 genomes]
rs13345307	1.00[ASN][1000 genomes]
rs1541926	1.00[ASN][1000 genomes]
rs16979688	1.00[ASN][1000 genomes]
rs17562787	1.00[ASN][1000 genomes]
rs17642665	1.00[ASN][1000 genomes]
rs1982077	1.00[ASN][1000 genomes]
rs2003183	1.00[ASN][1000 genomes]
rs2003345	1.00[ASN][1000 genomes]
rs2004356	1.00[ASN][1000 genomes]
rs2011438	1.00[ASN][1000 genomes]
rs2041261	1.00[ASN][1000 genomes]
rs2041263	1.00[ASN][1000 genomes]
rs2043320	1.00[ASN][1000 genomes]
rs2060252	1.00[ASN][1000 genomes]
rs2060253	1.00[ASN][1000 genomes]
rs28404390	1.00[ASN][1000 genomes]
rs28657408	1.00[ASN][1000 genomes]
rs28706378	1.00[ASN][1000 genomes]
rs28719739	1.00[ASN][1000 genomes]
rs35904300	1.00[ASN][1000 genomes]
rs3916871	1.00[MEX][hapmap]
rs3916881	1.00[MEX][hapmap]
rs4427916	1.00[ASN][1000 genomes]
rs4608431	1.00[ASN][1000 genomes]
rs4803798	1.00[ASN][1000 genomes]
rs58260098	1.00[ASN][1000 genomes]
rs58600209	1.00[ASN][1000 genomes]
rs58854055	1.00[ASN][1000 genomes]
rs58880456	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59240271	1.00[ASN][1000 genomes]
rs60372869	1.00[ASN][1000 genomes]
rs60455813	1.00[ASN][1000 genomes]
rs61531804	1.00[ASN][1000 genomes]
rs7251651	1.00[ASN][1000 genomes]
rs7254138	1.00[ASN][1000 genomes]
rs7257087	1.00[MEX][hapmap]
rs7257599	1.00[ASN][1000 genomes]
rs733289	1.00[ASN][1000 genomes]
rs73562250	1.00[ASN][1000 genomes]
rs73562267	1.00[ASN][1000 genomes]
rs73562286	1.00[ASN][1000 genomes]
rs73939607	1.00[ASN][1000 genomes]
rs747646	1.00[ASN][1000 genomes]
rs747647	1.00[ASN][1000 genomes]
rs754364	1.00[ASN][1000 genomes]
rs754365	1.00[ASN][1000 genomes]
rs754367	1.00[ASN][1000 genomes]
rs8101046	1.00[ASN][1000 genomes]
rs8111966	0.83[AMR][1000 genomes]
rs892133	1.00[ASN][1000 genomes]
rs9653111	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv912144	chr19:45636319-45687446	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv522341	chr19:45640124-45664218	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv1795888	chr19:45650386-45681988	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv520051	chr19:45660136-45664218	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45657600-45662000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr19:45657800-45663800	Weak transcription	Gastric	stomach
3	chr19:45657800-45663800	Weak transcription	Pancreas	Pancrea
4	chr19:45657800-45668200	Weak transcription	Right Atrium	heart
5	chr19:45658000-45662200	Weak transcription	HUVEC	blood vessel
6	chr19:45659200-45663400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:45659400-45661800	Enhancers	Esophagus	oesophagus
8	chr19:45660200-45661800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr19:45660200-45674000	Weak transcription	A549	lung
10	chr19:45660400-45663400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr19:45660600-45661800	Bivalent Enhancer	HepG2	liver
12	chr19:45661000-45664000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:45661200-45661800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:45661200-45661800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr19:45661200-45662000	Enhancers	Spleen	Spleen
16	chr19:45661400-45661600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr19:45661400-45661800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr19:45661400-45662000	Bivalent Enhancer	Duodenum Mucosa	Duodenum

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