Variant report

Variant	rs13401304
Chromosome Location	chr2:187395115-187395116
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:187393393..187396290-chr2:187445329..187448108,2	MCF-7	breast:
2	chr2:187392275..187395253-chr2:187409654..187411697,2	MCF-7	breast:
3	chr2:187386798..187388432-chr2:187393071..187395661,2	K562	blood:
4	chr2:187392659..187395517-chr2:187406680..187408986,2	MCF-7	breast:
5	chr2:187350468..187353373-chr2:187393682..187395846,2	K562	blood:
6	chr2:187388812..187391488-chr2:187392591..187395983,4	K562	blood:
7	chr2:187393911..187396398-chr2:187454708..187456930,2	K562	blood:

Variant related genes	Relation type
ENSG00000138448	Chromatin interaction
ENSG00000065548	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10177153	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10181681	0.91[EUR][1000 genomes]
rs10190003	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10198525	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10200749	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1037241	0.80[EUR][1000 genomes]
rs10497671	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10497672	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs11675633	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11675656	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678950	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680486	0.80[EUR][1000 genomes]
rs11690758	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11692347	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11693797	0.80[EUR][1000 genomes]
rs11888432	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901465	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11903027	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13392819	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]
rs13394241	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13428033	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1448848	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]
rs1448849	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1448855	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16827968	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16827994	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868383	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1869031	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2084488	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2084490	0.80[EUR][1000 genomes]
rs2197139	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2370688	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2887826	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35642346	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55719959	0.80[EUR][1000 genomes]
rs56137171	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61226319	0.80[EUR][1000 genomes]
rs61434493	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6434174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6709401	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6716324	0.80[EUR][1000 genomes]
rs6717525	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs6728382	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6731567	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs6744717	0.95[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]
rs72895449	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72897386	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72901315	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72901322	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579259	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7584137	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7603088	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917285	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
3	nsv459988	chr2:187364878-187440683	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv584031	chr2:187364878-187440683	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1004309	chr2:187389880-187455946	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv536082	chr2:187389880-187455946	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv875552	chr2:187393729-187505486	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13401304	ZC3H15	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187363000-187408800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:187363200-187397600	Weak transcription	Small Intestine	intestine
3	chr2:187367200-187396800	Weak transcription	Gastric	stomach
4	chr2:187367200-187405800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:187371000-187395800	Weak transcription	Fetal Heart	heart
6	chr2:187371000-187407800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:187373600-187395800	Weak transcription	HSMMtube	muscle
8	chr2:187373600-187397600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:187374400-187396200	Weak transcription	Brain Substantia Nigra	brain
10	chr2:187374400-187398800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:187377200-187397200	Weak transcription	HUVEC	blood vessel
12	chr2:187379000-187397400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:187381800-187406600	Weak transcription	NHEK	skin
14	chr2:187383000-187397000	Weak transcription	K562	blood
15	chr2:187383400-187397600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:187384200-187397800	Weak transcription	A549	lung
17	chr2:187386200-187395800	Weak transcription	NH-A	brain
18	chr2:187386200-187397000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:187386200-187397400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:187386200-187398400	Weak transcription	Liver	Liver
21	chr2:187386200-187405200	Weak transcription	HSMM	muscle
22	chr2:187386200-187408000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:187386800-187397400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:187386800-187397400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:187386800-187397600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:187387000-187395600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:187387200-187397400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:187387400-187397600	Weak transcription	Fetal Intestine Small	intestine
29	chr2:187388000-187399000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:187389400-187396200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:187394800-187395400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:187394800-187396400	Enhancers	HepG2	liver

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