Variant report

Variant	rs17012234
Chromosome Location	chr4:87911691-87911692
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10023056	0.90[CEU][hapmap]
rs10032244	0.90[CEU][hapmap]
rs10032710	0.90[CEU][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap]
rs10516785	0.90[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs10516786	0.90[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap];0.85[ASN][1000 genomes]
rs10516788	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1471251	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs151451	0.94[CEU][hapmap]
rs17012170	0.80[ASN][1000 genomes]
rs17012200	0.90[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.80[TSI][hapmap];0.87[ASN][1000 genomes]
rs17012213	0.87[ASN][1000 genomes]
rs17012216	0.85[ASN][1000 genomes]
rs17012334	0.90[CEU][hapmap]
rs17604480	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17701999	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17751557	0.80[TSI][hapmap]
rs17752307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1842685	0.90[CEU][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap]
rs236676	0.84[CEU][hapmap];0.94[GIH][hapmap];0.80[TSI][hapmap]
rs340633	0.85[CEU][hapmap]
rs340637	0.90[CEU][hapmap]
rs340638	0.90[CEU][hapmap]
rs340642	0.90[CEU][hapmap]
rs340643	0.90[CEU][hapmap]
rs340650	0.90[CEU][hapmap]
rs3733377	0.90[CEU][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap]
rs3736668	0.84[CEU][hapmap]
rs3755980	0.84[CEU][hapmap];0.94[GIH][hapmap];0.80[TSI][hapmap]
rs4693795	0.84[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs4693801	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4693802	0.94[GIH][hapmap];0.85[TSI][hapmap]
rs55787557	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55851914	0.85[ASN][1000 genomes]
rs55879154	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55913164	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56023922	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56050898	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56201818	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56378441	0.83[ASN][1000 genomes]
rs56390363	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56395939	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56406125	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6531941	0.80[TSI][hapmap]
rs6819155	0.81[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6839933	0.89[CEU][hapmap]
rs6840258	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6854749	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72667735	0.87[ASN][1000 genomes]
rs72667736	0.87[ASN][1000 genomes]
rs72667737	0.87[ASN][1000 genomes]
rs72667739	0.87[ASN][1000 genomes]
rs72667741	0.83[ASN][1000 genomes]
rs72667747	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667748	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667750	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667751	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72667752	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72667753	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72667754	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72667757	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72667759	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72667765	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7665282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs767315	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7682652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695426	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17012234	HSD17B13	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:87882600-87920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:87882800-87912400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:87892400-87920600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr4:87894600-87915600	Weak transcription	Lung	lung
6	chr4:87894600-87921000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:87895400-87920000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:87896200-87916000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:87896200-87919200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:87896800-87918800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:87897600-87915600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:87898200-87915400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:87899000-87915400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:87899000-87915400	Weak transcription	Left Ventricle	heart
15	chr4:87899000-87920600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr4:87899000-87921200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:87899200-87913200	Weak transcription	Liver	Liver
18	chr4:87899200-87920800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:87899200-87922800	Weak transcription	Osteobl	bone
20	chr4:87899200-87925800	Weak transcription	Hela-S3	cervix
21	chr4:87899200-87926600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:87900000-87915600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:87900000-87924400	Weak transcription	NHEK	skin
24	chr4:87900200-87920800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:87901000-87913000	Weak transcription	Fetal Intestine Large	intestine
26	chr4:87901200-87913200	Weak transcription	HepG2	liver
27	chr4:87903200-87918800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:87903200-87926200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr4:87903400-87915400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr4:87903600-87915400	Weak transcription	Thymus	Thymus
31	chr4:87903600-87915400	Weak transcription	Dnd41	blood
32	chr4:87903600-87919800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr4:87903600-87921000	Weak transcription	Primary T cells from cord blood	blood
34	chr4:87903800-87913000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:87903800-87915600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:87903800-87919800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr4:87903800-87920000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr4:87904000-87915200	Weak transcription	Fetal Thymus	thymus
39	chr4:87904200-87926200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr4:87904400-87912800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr4:87904400-87915800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:87904400-87920000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr4:87904600-87915800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr4:87904600-87917800	Weak transcription	Primary B cells from cord blood	blood
45	chr4:87904600-87921000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr4:87904800-87915000	Weak transcription	Fetal Intestine Small	intestine
47	chr4:87905800-87913000	Weak transcription	Placenta	Placenta
48	chr4:87905800-87920200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:87907600-87920000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr4:87908800-87914200	Weak transcription	Stomach Mucosa	stomach

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