Variant report

Variant	rs10032710
Chromosome Location	chr4:88066259-88066260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87855857..87857774-chr4:88064541..88066623,2	MCF-7	breast:
2	chr4:88066236..88067961-chr4:88070218..88071867,2	K562	blood:
3	chr4:87926495..87928144-chr4:88064956..88066726,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL8-2	chr4:88065070-88066502	ucscGeneNc_uc003hqf_1

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10023056	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10029254	1.00[YRI][hapmap]
rs10029915	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10034849	1.00[YRI][hapmap]
rs10433937	1.00[YRI][hapmap]
rs10516788	0.90[CEU][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap]
rs13118664	1.00[YRI][hapmap]
rs13120301	0.84[JPT][hapmap]
rs13130041	1.00[YRI][hapmap]
rs1481947	1.00[ASW][hapmap];0.95[MEX][hapmap]
rs151450	0.82[ASN][1000 genomes]
rs151451	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1552144	1.00[ASW][hapmap];0.94[MEX][hapmap]
rs17012234	0.90[CEU][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap]
rs17012334	0.90[CEU][hapmap]
rs17012512	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17012516	0.80[AMR][1000 genomes]
rs17605615	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs17701999	0.90[CEU][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap]
rs17752307	0.90[CEU][hapmap]
rs1842685	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2035403	0.84[ASN][1000 genomes]
rs2280954	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs236676	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs236681	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs28670747	0.81[AFR][1000 genomes]
rs3193672	1.00[ASW][hapmap];0.95[MEX][hapmap]
rs3733377	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3736668	0.95[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap]
rs3755980	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755983	0.83[CEU][hapmap];0.89[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3755985	0.90[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3775209	0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3775211	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3775226	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs3775228	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs4577539	1.00[ASW][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4693802	0.82[GIH][hapmap]
rs60695258	0.84[ASN][1000 genomes]
rs66477840	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6819155	0.90[CEU][hapmap];0.88[GIH][hapmap]
rs6840258	0.89[CEU][hapmap]
rs6854749	0.90[CEU][hapmap]
rs7665282	0.90[CEU][hapmap]
rs767315	0.89[CEU][hapmap]
rs7682652	0.90[CEU][hapmap]
rs9992651	1.00[YRI][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10032710	HSD17B13	cis	cerebellum	SCAN
rs10032710	HSD17B13	cis	parietal	SCAN
rs10032710	SLC10A6	cis	cerebellum	SCAN
rs10032710	HSD17B13	cis	multi-tissue	Pritchard

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88019000-88072200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:88042800-88069400	Strong transcription	Placenta	Placenta
3	chr4:88044600-88067600	Strong transcription	Primary B cells from cord blood	blood
4	chr4:88045800-88067600	Strong transcription	Fetal Thymus	thymus
5	chr4:88047200-88067000	Strong transcription	Liver	Liver
6	chr4:88053600-88082000	Weak transcription	HSMM	muscle
7	chr4:88054400-88066800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:88055200-88102800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:88055400-88072200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr4:88055600-88072200	Weak transcription	Fetal Kidney	kidney
11	chr4:88055800-88068200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:88056200-88067400	Weak transcription	HSMMtube	muscle
13	chr4:88056600-88090600	Weak transcription	Brain Angular Gyrus	brain
14	chr4:88057800-88068800	Weak transcription	Right Ventricle	heart
15	chr4:88057800-88072600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:88057800-88073800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:88057800-88074000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:88058200-88066600	Weak transcription	NHEK	skin
19	chr4:88058200-88067200	Weak transcription	Aorta	Aorta
20	chr4:88058200-88067400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:88058200-88068000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:88058200-88068600	Weak transcription	Gastric	stomach
23	chr4:88058200-88082400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:88058200-88109000	Weak transcription	Lung	lung
25	chr4:88058400-88068000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:88058400-88074000	Weak transcription	Hela-S3	cervix
27	chr4:88058600-88070200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:88058600-88071800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:88058600-88084200	Weak transcription	Brain Anterior Caudate	brain
30	chr4:88058800-88069400	Weak transcription	Brain Substantia Nigra	brain
31	chr4:88058800-88073400	Weak transcription	Fetal Muscle Leg	muscle
32	chr4:88058800-88082400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr4:88058800-88088400	Weak transcription	Thymus	Thymus
34	chr4:88058800-88092200	Weak transcription	Colonic Mucosa	Colon
35	chr4:88059000-88086600	Weak transcription	A549	lung
36	chr4:88059200-88068600	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:88059200-88071400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr4:88059200-88073600	Weak transcription	Pancreas	Pancrea
39	chr4:88059200-88087800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:88059200-88088000	Weak transcription	Fetal Stomach	stomach
41	chr4:88059200-88100800	Weak transcription	Osteobl	bone
42	chr4:88060800-88067200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr4:88061200-88082200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:88061400-88084000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:88061400-88109400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr4:88062200-88066600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:88062600-88072200	Weak transcription	NHDF-Ad	bronchial
48	chr4:88062600-88084400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:88062800-88066800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr4:88062800-88070000	Weak transcription	Stomach Smooth Muscle	stomach

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