Variant report

Variant	rs3193672
Chromosome Location	chr4:88083107-88083108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88080915..88083555-chr4:88157675..88159786,2	K562	blood:
2	chr4:88082449..88084171-chr4:88140613..88143085,2	K562	blood:

Variant related genes	Relation type
ENSG00000145332	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10000784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10025704	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10032710	1.00[ASW][hapmap];0.95[MEX][hapmap]
rs1021104	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11946293	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13435265	0.83[AMR][1000 genomes]
rs1481947	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17012516	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17012517	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1842685	0.89[MEX][hapmap]
rs28505236	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28571134	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28670747	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28734493	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28882732	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3209390	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3733377	0.84[MEX][hapmap]
rs3755980	1.00[ASW][hapmap];0.89[MEX][hapmap]
rs4577539	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55747890	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66527077	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72667790	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7437661	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv879526	chr4:88062611-88087832	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3193672	HSD17B13	cis	cerebellum	SCAN
rs3193672	HSD17B13	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88055200-88102800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:88056600-88090600	Weak transcription	Brain Angular Gyrus	brain
3	chr4:88058200-88109000	Weak transcription	Lung	lung
4	chr4:88058600-88084200	Weak transcription	Brain Anterior Caudate	brain
5	chr4:88058800-88088400	Weak transcription	Thymus	Thymus
6	chr4:88058800-88092200	Weak transcription	Colonic Mucosa	Colon
7	chr4:88059000-88086600	Weak transcription	A549	lung
8	chr4:88059200-88087800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:88059200-88088000	Weak transcription	Fetal Stomach	stomach
10	chr4:88059200-88100800	Weak transcription	Osteobl	bone
11	chr4:88061400-88084000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:88061400-88109400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:88062600-88084400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr4:88063000-88090800	Weak transcription	Left Ventricle	heart
15	chr4:88063000-88090800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:88063200-88088400	Weak transcription	Ovary	ovary
17	chr4:88063200-88097400	Weak transcription	Small Intestine	intestine
18	chr4:88063200-88102000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:88063800-88083600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:88063800-88087800	Weak transcription	Primary T cells from cord blood	blood
21	chr4:88064200-88090000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr4:88064200-88098800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:88064200-88100400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr4:88064400-88084400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:88064400-88092600	Weak transcription	HUVEC	blood vessel
26	chr4:88065600-88088200	Weak transcription	GM12878-XiMat	blood
27	chr4:88066200-88097200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:88066200-88101000	Weak transcription	HMEC	breast
29	chr4:88066600-88084000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:88066600-88089800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:88066800-88084200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr4:88066800-88084400	Weak transcription	K562	blood
33	chr4:88066800-88084600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:88066800-88093000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr4:88067000-88089400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:88067600-88084400	Weak transcription	Primary B cells from cord blood	blood
37	chr4:88067600-88087400	Weak transcription	Fetal Thymus	thymus
38	chr4:88067600-88096800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:88067800-88084400	Weak transcription	Dnd41	blood
40	chr4:88068000-88116400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr4:88068200-88087000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr4:88068600-88084200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:88073000-88087600	Weak transcription	Adipose Nuclei	Adipose
44	chr4:88073000-88089400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr4:88073400-88084200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:88073400-88093400	Weak transcription	Fetal Kidney	kidney
47	chr4:88073400-88098200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:88073400-88113000	Weak transcription	NHDF-Ad	bronchial
49	chr4:88073800-88090800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr4:88074000-88100400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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