Variant report

Variant	rs6531941
Chromosome Location	chr4:87895960-87895961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87894083..87901163-chr4:87926378..87930735,13	K562	blood:
2	chr4:87895920..87900923-chr4:87925411..87930708,9	MCF-7	breast:
3	chr4:87892847..87896142-chr4:87913687..87916404,3	K562	blood:
4	chr4:87894580..87900721-chr4:87926553..87929375,8	MCF-7	breast:
5	chr4:87876640..87879559-chr4:87894378..87897359,2	K562	blood:
6	chr4:87882295..87884551-chr4:87895406..87897794,3	K562	blood:
7	chr4:87858518..87860018-chr4:87894461..87896898,2	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10015639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10032244	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10050311	0.87[CEU][hapmap]
rs1010902	0.85[EUR][1000 genomes]
rs1010903	0.86[EUR][1000 genomes]
rs10516786	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10516788	0.80[TSI][hapmap]
rs11729622	0.84[ASN][1000 genomes]
rs13126334	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs13127250	0.84[ASN][1000 genomes]
rs1447994	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17012170	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs17012200	1.00[CEU][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17012213	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17012216	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17012234	0.80[TSI][hapmap]
rs17694112	0.81[CEU][hapmap]
rs17701999	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	0.84[EUR][1000 genomes]
rs1985944	0.86[EUR][1000 genomes]
rs2053769	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2053770	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2053771	0.95[EUR][1000 genomes]
rs2287147	0.81[CEU][hapmap]
rs340626	0.81[ASN][1000 genomes]
rs340630	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs340633	0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs340636	0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs340637	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs340638	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs340639	0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs340641	0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs340642	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs340643	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs340648	0.84[ASN][1000 genomes]
rs340650	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs375795	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs388401	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs4693153	0.93[EUR][1000 genomes]
rs4693154	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs4693795	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4693796	0.91[ASN][1000 genomes]
rs4693798	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4693800	0.84[ASN][1000 genomes]
rs55698195	0.84[EUR][1000 genomes]
rs55831707	0.93[EUR][1000 genomes]
rs55851914	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55913164	0.84[EUR][1000 genomes]
rs56201068	0.84[EUR][1000 genomes]
rs58633957	0.81[ASN][1000 genomes]
rs61651372	0.93[EUR][1000 genomes]
rs6531948	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs6811587	0.86[ASN][1000 genomes]
rs6819155	0.83[TSI][hapmap]
rs6839933	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
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]
rs72667735	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72667736	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72667737	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72667739	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72667741	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7657530	0.91[CHB][hapmap]
rs7665282	0.84[EUR][1000 genomes]
rs867196	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs9715807	0.84[ASN][1000 genomes]

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
rs6531941	HSD17B13	cis	cerebellum	SCAN

Chromatin state (count:95 , 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	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:87881000-87897600	Weak transcription	Brain Angular Gyrus	brain
4	chr4:87882400-87898600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:87882600-87920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:87882800-87912400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:87886600-87898600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:87888800-87898800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr4:87890200-87898600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr4:87891200-87896200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:87891400-87896000	Enhancers	Stomach Mucosa	stomach
12	chr4:87891600-87897600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr4:87892000-87900400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr4:87892200-87907000	Weak transcription	Brain Anterior Caudate	brain
15	chr4:87892400-87920600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr4:87892600-87896600	Enhancers	Dnd41	blood
17	chr4:87892600-87898400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:87892800-87898600	Weak transcription	Brain Hippocampus Middle	brain
19	chr4:87892800-87909400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:87893200-87896400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr4:87893200-87900200	Weak transcription	Esophagus	oesophagus
22	chr4:87893800-87896200	Enhancers	Primary hematopoietic stem cells	blood
23	chr4:87893800-87896600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr4:87894000-87896000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:87894000-87896400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr4:87894200-87897800	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr4:87894200-87899000	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr4:87894400-87897400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:87894400-87897600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr4:87894400-87898400	Weak transcription	Osteobl	bone
31	chr4:87894400-87898600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:87894400-87898600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr4:87894400-87911000	Weak transcription	Pancreas	Pancrea
34	chr4:87894600-87896400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:87894600-87897200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:87894600-87897200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:87894600-87897200	Weak transcription	Placenta	Placenta
38	chr4:87894600-87897200	Weak transcription	HMEC	breast
39	chr4:87894600-87897400	Weak transcription	Psoas Muscle	Psoas
40	chr4:87894600-87897800	Weak transcription	Colonic Mucosa	Colon
41	chr4:87894600-87898000	Weak transcription	Hela-S3	cervix
42	chr4:87894600-87898400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:87894600-87898600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:87894600-87898600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:87894600-87898600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr4:87894600-87898600	Weak transcription	Left Ventricle	heart
47	chr4:87894600-87898600	Weak transcription	Ovary	ovary
48	chr4:87894600-87898600	Weak transcription	Right Atrium	heart
49	chr4:87894600-87898800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:87894600-87898800	Weak transcription	Spleen	Spleen

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