Variant report

Variant	rs17181400
Chromosome Location	chr3:19992137-19992138
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr3:19992041-19992213	K562	blood:	n/a	n/a
2	CTCF	chr3:19992040-19992190	NHDF-neo	bronchial:	n/a	n/a
3	POLR2A	chr3:19986265-20000717	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:19986921..19992254-chr3:20078952..20084327,16	K562	blood:
2	chr3:19987383..19992426-chr3:20011245..20019650,13	MCF-7	breast:
3	chr3:19987439..19992261-chr3:20226257..20229350,4	K562	blood:
4	chr3:19991110..19993492-chr3:20053410..20056377,2	K562	blood:
5	chr3:19986985..19992254-chr3:20079680..20083856,14	K562	blood:

No data

Variant related genes	Relation type
EFHB	TF binding region
RAB5A	TF binding region
ENSG00000229468	Chromatin interaction
ENSG00000129810	Chromatin interaction
ENSG00000114166	Chromatin interaction
ENSG00000183977	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11128927	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11128928	0.94[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11128929	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11128930	0.94[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11128931	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1143451	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12629485	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12631435	0.82[EUR][1000 genomes]
rs13065319	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13068289	0.81[EUR][1000 genomes]
rs13070718	0.83[EUR][1000 genomes]
rs13072891	0.81[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs13076973	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13077307	0.85[ASN][1000 genomes]
rs13078505	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13082980	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13086159	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13089853	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13093485	0.81[EUR][1000 genomes]
rs13097697	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13098388	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17181862	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17796115	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34305656	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34343204	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34417128	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34705953	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34872212	0.81[EUR][1000 genomes]
rs35175665	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35684714	0.81[EUR][1000 genomes]
rs35713165	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4610240	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58859849	0.83[ASN][1000 genomes]
rs59086970	0.88[ASN][1000 genomes]
rs59608170	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60255931	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6796425	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71316239	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7434271	0.97[EUR][1000 genomes]
rs7614695	0.83[ASN][1000 genomes]
rs7615145	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7618928	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7633940	0.83[ASN][1000 genomes]
rs7634934	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7646128	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9877801	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9878879	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17181400	EFHB	cis	Adipose Subcutaneous	GTEx
rs17181400	EFHB	cis	Artery Tibial	GTEx
rs17181400	EFHB	cis	Thyroid	GTEx
rs17181400	EFHB	cis	Muscle Skeletal	GTEx
rs17181400	EFHB	cis	multi-tissue	Pritchard
rs17181400	EFHB	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19989800-19993000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:19989800-19993000	Weak transcription	Esophagus	oesophagus
3	chr3:19989800-19993000	Weak transcription	Spleen	Spleen
4	chr3:19989800-19995000	Weak transcription	Gastric	stomach
5	chr3:19989800-20018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:19990000-19992600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:19990000-19993400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr3:19990000-20008600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:19990000-20016200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:19990200-19992200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:19990600-19992200	Enhancers	Liver	Liver
12	chr3:19990800-19992400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:19990800-19993000	Weak transcription	Fetal Stomach	stomach
14	chr3:19990800-19996600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
15	chr3:19990800-20017000	Weak transcription	Fetal Kidney	kidney
16	chr3:19991000-19992200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:19991000-19992200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:19991000-19992200	Enhancers	Adipose Nuclei	Adipose
19	chr3:19991000-19992400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:19991000-19992400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:19991000-19992400	Active TSS	GM12878-XiMat	blood
22	chr3:19991000-19992600	Weak transcription	HSMM	muscle
23	chr3:19991000-19993000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:19991000-19993000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:19991000-19993000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:19991000-19993000	Weak transcription	Right Atrium	heart
27	chr3:19991000-19993000	Weak transcription	Thymus	Thymus
28	chr3:19991000-19993200	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:19991000-19993200	Weak transcription	HSMMtube	muscle
30	chr3:19991000-19995200	Weak transcription	Brain Germinal Matrix	brain
31	chr3:19991000-19996200	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:19991000-19996600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:19991000-20001800	Weak transcription	Brain Angular Gyrus	brain
34	chr3:19991200-19992400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:19991200-19992400	Weak transcription	Osteobl	bone
36	chr3:19991200-19992600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:19991200-19992800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:19991200-19993000	Weak transcription	Brain Anterior Caudate	brain
39	chr3:19991200-19993200	Weak transcription	Primary B cells from cord blood	blood
40	chr3:19991200-20002600	Weak transcription	Fetal Heart	heart
41	chr3:19991400-19992200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr3:19991400-19992400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:19991400-19992400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:19991400-19992400	Active TSS	NHLF	lung
45	chr3:19991400-19992600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:19991400-19992800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:19991400-19992800	Weak transcription	Fetal Brain Male	brain
48	chr3:19991400-19993000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr3:19991400-19993000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:19991400-19993200	Weak transcription	Right Ventricle	heart

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