Variant report

Variant	rs1745300
Chromosome Location	chr4:74447104-74447105
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10009048	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10011419	0.85[AMR][1000 genomes]
rs10011536	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10019146	0.95[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs10019320	0.85[AMR][1000 genomes]
rs10020054	0.85[AMR][1000 genomes]
rs10021827	0.85[AMR][1000 genomes]
rs10029673	0.85[AMR][1000 genomes]
rs10938088	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11729144	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247659	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1247668	0.92[YRI][hapmap];0.87[AMR][1000 genomes]
rs1247670	0.86[MEX][hapmap]
rs1247671	0.86[MEX][hapmap]
rs12503916	1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs12505842	0.85[AMR][1000 genomes]
rs12506668	0.85[AMR][1000 genomes]
rs12506675	0.85[AMR][1000 genomes]
rs12507775	1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs1271392	0.82[GIH][hapmap]
rs13135124	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13144296	0.85[AMR][1000 genomes]
rs13149172	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1528915	0.85[AMR][1000 genomes]
rs1528916	0.85[AMR][1000 genomes]
rs1528917	0.85[AMR][1000 genomes]
rs1528918	0.85[AMR][1000 genomes]
rs1569204	0.81[MEX][hapmap]
rs1569207	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849628	1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs16849629	0.85[AMR][1000 genomes]
rs16849651	0.85[AMR][1000 genomes]
rs16849656	0.85[AMR][1000 genomes]
rs16849659	0.85[AMR][1000 genomes]
rs16849675	0.85[AMR][1000 genomes]
rs16849677	0.85[AMR][1000 genomes]
rs16849727	0.83[MEX][hapmap]
rs2008288	0.85[AMR][1000 genomes]
rs28407399	0.85[AMR][1000 genomes]
rs28450939	0.85[AMR][1000 genomes]
rs28612539	0.85[AMR][1000 genomes]
rs28693538	0.85[AMR][1000 genomes]
rs34773614	0.85[AMR][1000 genomes]
rs34859660	0.85[AMR][1000 genomes]
rs62312137	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665563	0.85[AMR][1000 genomes]
rs7665972	0.84[AMR][1000 genomes]
rs7667019	0.85[AMR][1000 genomes]
rs7667185	0.82[AMR][1000 genomes]
rs7674913	0.82[AMR][1000 genomes]
rs7676850	0.85[AMR][1000 genomes]
rs7676870	0.85[AMR][1000 genomes]
rs7676884	0.85[AMR][1000 genomes]
rs7682201	0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs7695792	0.85[AMR][1000 genomes]
rs7695946	0.85[AMR][1000 genomes]
rs7696502	0.85[AMR][1000 genomes]
rs997478	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999939	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1792624	chr4:74437054-74453857	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1745300	ART3	cis	cerebellum	SCAN
rs1745300	MUC7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74438000-74464800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:74439000-74448400	Weak transcription	Fetal Intestine Large	intestine
3	chr4:74439800-74448600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:74440200-74449000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:74440200-74449600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:74440200-74451200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:74440200-74455200	Weak transcription	Fetal Intestine Small	intestine
8	chr4:74440200-74457400	Weak transcription	Pancreas	Pancrea
9	chr4:74440200-74472600	Weak transcription	Gastric	stomach
10	chr4:74441200-74464800	Weak transcription	Placenta	Placenta
11	chr4:74442200-74450200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr4:74442600-74449400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:74442800-74448800	Weak transcription	HMEC	breast
14	chr4:74443600-74455400	Weak transcription	Stomach Mucosa	stomach
15	chr4:74446200-74456000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr4:74446400-74451000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:74447000-74447400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr4:74447000-74447400	Strong transcription	Pancreatic Islets	Pancreatic Islet
19	chr4:74447000-74447600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr4:74447000-74447600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr4:74447000-74447600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr4:74447000-74447600	Strong transcription	Thymus	Thymus
23	chr4:74447000-74447800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr4:74447000-74449400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:74447000-74456000	Strong transcription	Fetal Thymus	thymus

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