Variant report

Variant	rs13392819
Chromosome Location	chr2:187347385-187347386
allele	G/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	JUND	chr2:187347240-187347582	HepG2	liver:	n/a	chr2:187347406-187347417
2	MAZ	chr2:187347199-187347441	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:187347068..187348940-chr2:187349193..187350808,2	MCF-7	breast:

Variant related genes	Relation type
ZC3H15	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10177153	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10178888	0.88[EUR][1000 genomes]
rs10190003	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10196955	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10198525	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10200749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10208643	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1037241	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10497671	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10497672	0.91[CEU][hapmap]
rs11675633	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675656	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11678950	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11680486	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11688988	0.89[ASN][1000 genomes]
rs11690758	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11692028	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11692347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693797	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11888432	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11895483	0.85[EUR][1000 genomes]
rs11898666	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11901465	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903027	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328822	0.89[ASN][1000 genomes]
rs13393891	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13394241	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13397188	0.89[ASN][1000 genomes]
rs13401304	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13428033	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1448848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1448849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1448855	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16827968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16827994	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1868383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869031	0.81[EUR][1000 genomes]
rs2044683	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2084488	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084489	0.89[ASN][1000 genomes]
rs2084490	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2197139	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2370688	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2887826	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35642346	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55719959	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56137171	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61226319	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61434493	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434167	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6434174	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6709401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6716324	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6717525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721789	0.89[ASN][1000 genomes]
rs6724161	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6728382	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6744717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72893450	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72895449	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72897386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72901315	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72901322	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7579259	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585889	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7588607	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7597954	0.89[ASN][1000 genomes]
rs7603088	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9288129	0.89[ASN][1000 genomes]
rs9917285	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13392819	ZC3H15	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187320600-187347400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:187328000-187350400	Weak transcription	Pancreas	Pancrea
3	chr2:187337000-187348000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr2:187339800-187347400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:187339800-187348400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:187339800-187349800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:187344000-187348000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:187345000-187347400	Enhancers	NHEK	skin
9	chr2:187346200-187348200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:187346400-187347600	Weak transcription	Fetal Intestine Small	intestine
11	chr2:187346400-187348600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:187346400-187348600	Weak transcription	HMEC	breast
13	chr2:187346400-187349200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:187346600-187348200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:187346600-187350000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:187347000-187348400	Enhancers	HepG2	liver

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