Variant report

Variant	rs10516786
Chromosome Location	chr4:87892341-87892342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87885535..87895894-chr4:87923652..87929924,15	K562	blood:
2	chr4:87890335..87892797-chr4:87926492..87928312,3	MCF-7	breast:
3	chr4:87891928..87895544-chr4:87897508..87902479,6	K562	blood:
4	chr4:87853531..87856106-chr4:87889167..87893034,3	K562	blood:
5	chr4:87891330..87894052-chr4:87927164..87929617,3	K562	blood:

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10015639	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10050311	0.87[CEU][hapmap]
rs1010902	0.85[EUR][1000 genomes]
rs1010903	0.86[EUR][1000 genomes]
rs10516785	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10516788	0.85[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap]
rs1447994	0.84[EUR][1000 genomes]
rs1471251	0.94[CHD][hapmap];0.94[JPT][hapmap]
rs17012170	0.92[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17012200	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17012213	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17012216	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17012234	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]
rs17694112	0.81[CEU][hapmap]
rs17701999	0.80[ASW][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap]
rs17751427	0.92[EUR][1000 genomes]
rs17751557	0.93[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs17752307	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1985944	0.86[EUR][1000 genomes]
rs2053771	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2287147	0.81[CEU][hapmap]
rs4693153	0.93[EUR][1000 genomes]
rs4693154	0.93[CEU][hapmap];0.85[CHB][hapmap];0.93[EUR][1000 genomes]
rs4693795	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4693801	0.86[ASN][1000 genomes]
rs55698195	0.84[EUR][1000 genomes]
rs55831707	0.93[EUR][1000 genomes]
rs55851914	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55879154	0.85[ASN][1000 genomes]
rs55913164	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56023922	0.82[ASN][1000 genomes]
rs56201068	0.84[EUR][1000 genomes]
rs56378441	0.87[ASN][1000 genomes]
rs56390363	0.84[ASN][1000 genomes]
rs56406125	0.84[ASN][1000 genomes]
rs61651372	0.93[EUR][1000 genomes]
rs6531941	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6819155	0.94[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs6840258	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs6854749	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs72667703	0.86[EUR][1000 genomes]
rs72667705	0.85[EUR][1000 genomes]
rs72667716	0.93[EUR][1000 genomes]
rs72667721	0.93[EUR][1000 genomes]
rs72667724	0.93[EUR][1000 genomes]
rs72667727	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72667735	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667736	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667737	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667739	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667741	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667747	0.86[ASN][1000 genomes]
rs72667748	0.86[ASN][1000 genomes]
rs72667750	0.86[ASN][1000 genomes]
rs72667751	0.84[ASN][1000 genomes]
rs72667752	0.84[ASN][1000 genomes]
rs72667753	0.84[ASN][1000 genomes]
rs72667754	0.84[ASN][1000 genomes]
rs7665282	0.89[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs767315	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7682652	0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7695426	0.86[ASN][1000 genomes]
rs9799529	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10516786	HSD17B13	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87868600-87898000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:87869800-87894000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:87881000-87897600	Weak transcription	Brain Angular Gyrus	brain
5	chr4:87882000-87895400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:87882200-87895600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:87882400-87893800	Weak transcription	Colonic Mucosa	Colon
8	chr4:87882400-87898600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:87882600-87920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:87882800-87912400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:87883800-87894200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:87884200-87893800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:87884200-87894000	Weak transcription	Fetal Intestine Small	intestine
14	chr4:87885000-87894200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:87885000-87894200	Weak transcription	HMEC	breast
16	chr4:87886600-87898600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:87886800-87894200	Weak transcription	Hela-S3	cervix
18	chr4:87887000-87892600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:87888000-87893400	Enhancers	HUVEC	blood vessel
20	chr4:87888200-87895800	Weak transcription	Primary T cells from cord blood	blood
21	chr4:87888400-87895000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:87888600-87892400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:87888600-87893400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:87888600-87893400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr4:87888800-87898800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr4:87889200-87894000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr4:87889200-87894200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:87889200-87895400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr4:87889400-87894200	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr4:87889800-87892400	Weak transcription	Fetal Kidney	kidney
31	chr4:87889800-87893400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr4:87889800-87893800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr4:87890000-87893400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr4:87890000-87894000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:87890200-87898600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr4:87890400-87892600	Weak transcription	GM12878-XiMat	blood
37	chr4:87890400-87894000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:87890600-87893800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr4:87890600-87894200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr4:87891000-87895200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr4:87891200-87896200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:87891400-87892400	Enhancers	Ovary	ovary
43	chr4:87891400-87892400	Enhancers	A549	lung
44	chr4:87891400-87892600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr4:87891400-87892600	Enhancers	Gastric	stomach
46	chr4:87891400-87892600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr4:87891400-87893800	Enhancers	HepG2	liver
48	chr4:87891400-87894400	Enhancers	Liver	Liver
49	chr4:87891400-87894600	Enhancers	Psoas Muscle	Psoas
50	chr4:87891400-87896000	Enhancers	Stomach Mucosa	stomach

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