Variant report

Variant	rs4351013
Chromosome Location	chr4:86963784-86963785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10004712	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10009942	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10011390	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020650	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025882	1.00[ASN][1000 genomes]
rs10033283	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[ASN][1000 genomes]
rs10516763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103861	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13110593	1.00[ASN][1000 genomes]
rs13114632	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1436522	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1436524	1.00[CHB][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17008675	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011341	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[ASN][1000 genomes]
rs17011573	1.00[CHB][hapmap]
rs2043648	0.97[EUR][1000 genomes]
rs2043649	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap]
rs2043650	0.98[EUR][1000 genomes]
rs2060588	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2575674	1.00[ASN][1000 genomes]
rs2589518	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28398988	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28409011	0.83[ASN][1000 genomes]
rs28538338	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28660296	1.00[ASN][1000 genomes]
rs28756326	1.00[ASN][1000 genomes]
rs34725089	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34836858	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34929575	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35755826	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35833770	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35893712	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35971482	1.00[ASN][1000 genomes]
rs36047328	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775166	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs3775168	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs3775169	0.98[EUR][1000 genomes]
rs4345173	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382028	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4446299	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4479697	0.98[EUR][1000 genomes]
rs6531890	0.93[EUR][1000 genomes]
rs6531891	0.98[EUR][1000 genomes]
rs6531893	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66502717	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821840	1.00[ASN][1000 genomes]
rs6848433	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[ASN][1000 genomes]
rs6856450	0.98[EUR][1000 genomes]
rs71603477	1.00[ASN][1000 genomes]
rs71603479	1.00[ASN][1000 genomes]
rs7659520	1.00[ASN][1000 genomes]
rs7660160	1.00[ASN][1000 genomes]
rs7670470	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670681	1.00[ASN][1000 genomes]
rs7677101	1.00[ASN][1000 genomes]
rs7691896	0.96[EUR][1000 genomes]
rs7692460	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[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	nsv1009622	chr4:86893536-87119153	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1003585	chr4:86957967-87250436	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4351013	HSD17B13	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86916800-86985400	Weak transcription	Ovary	ovary
2	chr4:86936000-86975600	Weak transcription	Brain Germinal Matrix	brain
3	chr4:86936400-86990600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:86948200-86966600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:86949200-86988600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:86950600-86967000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:86955000-86964400	Weak transcription	Brain Anterior Caudate	brain
8	chr4:86955000-86966400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr4:86955000-86985000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:86955200-86964400	Weak transcription	Brain Substantia Nigra	brain
11	chr4:86955200-86964800	Weak transcription	Brain Angular Gyrus	brain
12	chr4:86955200-86965000	Weak transcription	Right Atrium	heart
13	chr4:86955200-86966600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr4:86955200-86971000	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:86955200-87003800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:86956200-86969600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:86958200-86975600	Weak transcription	Fetal Brain Female	brain
18	chr4:86958400-86992600	Weak transcription	Fetal Kidney	kidney
19	chr4:86958600-86965200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:86959200-86964400	Weak transcription	HSMMtube	muscle
21	chr4:86959600-86964600	Weak transcription	HUVEC	blood vessel
22	chr4:86960000-86964600	Weak transcription	Fetal Heart	heart
23	chr4:86961200-86979400	Weak transcription	Fetal Stomach	stomach
24	chr4:86961200-86981000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:86963000-86964600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:86963600-86966400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:86963600-86974400	Weak transcription	Fetal Lung	lung
28	chr4:86963600-86988800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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