Variant report

Variant	rs3796547
Chromosome Location	chr4:57181995-57181996
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10015221	0.89[JPT][hapmap]
rs10015634	0.89[JPT][hapmap]
rs10031550	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10034154	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10518	0.89[JPT][hapmap]
rs10866433	0.89[JPT][hapmap]
rs11733474	0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs12331363	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12331412	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13114104	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13133016	0.81[EUR][1000 genomes]
rs13141793	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs13147824	0.86[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1356788	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1401912	0.87[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1464286	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17051687	0.89[JPT][hapmap]
rs17086803	0.89[JPT][hapmap]
rs1976815	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1996650	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2030365	0.84[EUR][1000 genomes]
rs2049087	0.94[JPT][hapmap]
rs2139512	0.86[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs28559894	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2899063	0.87[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3796542	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3822003	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4073691	0.94[JPT][hapmap]
rs4167	0.87[CEU][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4305581	0.94[JPT][hapmap]
rs4865087	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4865100	0.80[AMR][1000 genomes]
rs4865101	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57503982	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59615456	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61750793	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs62310633	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554349	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs6554352	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6554355	0.87[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6554356	0.87[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6811821	0.89[JPT][hapmap]
rs6812041	0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6819534	0.94[JPT][hapmap]
rs6826795	0.82[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6841016	0.81[EUR][1000 genomes]
rs7657711	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7661712	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7683781	0.87[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7692385	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs7700034	0.84[JPT][hapmap]
rs9683679	0.87[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9684298	0.87[CEU][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9993277	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9996593	0.89[JPT][hapmap]
rs9997639	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription 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	88 gene(s)	inside rSNPs	diseases
6	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3796547	PPAT	cis	normal skin	skin_eQTL
rs3796547	PPAT	cis	uninvolved skin	skin_eQTL
rs3796547	AASDH	cis	parietal	SCAN
rs3796547	PPAT	cis	lymphoblastoid	seeQTL
rs3796547	USP46	cis	cerebellum	SCAN
rs3796547	AASDH	cis	cerebellum	SCAN
rs3796547	PPAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57162800-57189400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr4:57163000-57184000	Weak transcription	Right Atrium	heart
3	chr4:57167600-57203400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:57167800-57218600	Weak transcription	Small Intestine	intestine
5	chr4:57171000-57187400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:57172000-57204000	Weak transcription	Stomach Mucosa	stomach
7	chr4:57173200-57202800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:57173800-57182600	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr4:57173800-57185200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:57174400-57195000	Strong transcription	Fetal Intestine Small	intestine
11	chr4:57174400-57203800	Weak transcription	Fetal Kidney	kidney
12	chr4:57174600-57182200	Weak transcription	HepG2	liver
13	chr4:57174600-57197200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr4:57176000-57183400	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr4:57176000-57190000	Weak transcription	Gastric	stomach
16	chr4:57176600-57183200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:57177200-57183000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:57177400-57185200	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:57177600-57182200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:57177600-57215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:57177800-57183400	Strong transcription	Colonic Mucosa	Colon
22	chr4:57177800-57184000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:57177800-57184200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr4:57178000-57190400	Weak transcription	Brain Angular Gyrus	brain
25	chr4:57178200-57183600	Strong transcription	Fetal Stomach	stomach
26	chr4:57178200-57184400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr4:57178200-57189400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr4:57178200-57189800	Weak transcription	Brain Anterior Caudate	brain
29	chr4:57178200-57190000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr4:57178200-57190200	Weak transcription	Brain Substantia Nigra	brain
31	chr4:57178200-57211800	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:57178400-57182800	Weak transcription	Fetal Lung	lung
33	chr4:57178400-57183200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:57178600-57190200	Weak transcription	Fetal Brain Male	brain
35	chr4:57178800-57182200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr4:57178800-57183200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:57178800-57187000	Strong transcription	Fetal Brain Female	brain
38	chr4:57179000-57183000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:57179200-57182800	Strong transcription	Ovary	ovary
40	chr4:57179200-57183000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:57179200-57186200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:57179400-57183000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:57180000-57183400	Strong transcription	Brain Germinal Matrix	brain
44	chr4:57180200-57182000	ZNF genes & repeats	Placenta	Placenta
45	chr4:57180200-57182800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
46	chr4:57180400-57182600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr4:57180400-57183800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:57180400-57189800	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr4:57180600-57190000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:57180800-57191800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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