Variant report

Variant	rs13142103
Chromosome Location	chr4:55899286-55899287
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	POLR2A	chr4:55899095-55899389	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr4:55899266-55899860	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
RNU6-410P	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10018070	0.85[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13101523	0.95[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13112551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13144674	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13144875	0.90[ASN][1000 genomes]
rs28744674	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34227858	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4259119	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4333248	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4457012	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4566712	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4571397	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4577640	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4582210	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4596303	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap]
rs4864529	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864530	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5018667	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57528857	0.94[ASN][1000 genomes]
rs6554225	0.80[ASN][1000 genomes]
rs6554226	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6554228	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554229	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66459610	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66506770	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6816847	0.90[ASN][1000 genomes]
rs6820336	0.95[ASN][1000 genomes]
rs6820371	0.95[ASN][1000 genomes]
rs6844468	0.93[ASN][1000 genomes]
rs6845385	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7658751	0.80[ASN][1000 genomes]
rs7661259	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7677709	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7679094	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv829939	chr4:55856771-56005011	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv432603	chr4:55877236-55970782	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv524342	chr4:55891531-55921535	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13142103	SPATA18	cis	parietal	SCAN
rs13142103	GSX2	cis	cerebellum	SCAN
rs13142103	TMEM165	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55895800-55904600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr4:55896400-55904400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:55896800-55905000	Enhancers	HMEC	breast
4	chr4:55897800-55900000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:55898000-55902400	Weak transcription	NHEK	skin
6	chr4:55898200-55900400	Enhancers	Left Ventricle	heart
7	chr4:55898200-55902200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:55898400-55899800	Enhancers	Fetal Intestine Large	intestine
9	chr4:55898400-55900000	Enhancers	Fetal Intestine Small	intestine
10	chr4:55898600-55900000	Enhancers	Placenta	Placenta
11	chr4:55898600-55900200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:55898600-55900400	Enhancers	Lung	lung
13	chr4:55898600-55900400	Enhancers	Placenta Amnion	Placenta Amnion
14	chr4:55898600-55900800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:55898800-55899400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:55898800-55899600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:55898800-55899800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr4:55898800-55900200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr4:55898800-55900600	Enhancers	Fetal Lung	lung
20	chr4:55898800-55900800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr4:55899000-55899400	Enhancers	Duodenum Mucosa	Duodenum
22	chr4:55899000-55899800	Enhancers	Gastric	stomach
23	chr4:55899200-55900000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:55899200-55900400	Enhancers	Right Atrium	heart
25	chr4:55899200-55902600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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