Variant report

Variant	rs4589131
Chromosome Location	chr1:161167698-161167699
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:161166380-161172732	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr1:161167318-161169105	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:161167172-161169154	HUVEC	blood vessel:	n/a	n/a
4	MXI1	chr1:161166226-161169654	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr1:161166749-161167732	IMR90	lung:	n/a	n/a
6	POLR2A	chr1:161167555-161169518	HUVEC	blood vessel:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161146149..161148738-chr1:161166807..161168817,2	MCF-7	breast:
2	chr1:161166482..161168159-chr1:161197739..161199881,2	MCF-7	breast:
3	chr1:161147057..161148568-chr1:161166119..161168156,2	MCF-7	breast:
4	chr1:161166987..161169982-chr1:161170593..161173822,5	MCF-7	breast:
5	chr1:161130520..161133056-chr1:161166006..161167736,2	K562	blood:
6	chr1:161166242..161168991-chr1:161344064..161345577,2	MCF-7	breast:
7	chr1:161167464..161169651-chr1:161275959..161277953,2	K562	blood:

No data

Variant related genes	Relation type
ADAMTS4	TF binding region
NDUFS2	TF binding region
ENSG00000143258	Chromatin interaction
ENSG00000158850	Chromatin interaction
ENSG00000158864	Chromatin interaction
ENSG00000273075	Chromatin interaction
ENSG00000158882	Chromatin interaction
ENSG00000158887	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10797094	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11265564	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024799	1.00[JPT][hapmap]
rs2501876	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2502806	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs3813622	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073054	0.87[GIH][hapmap]
rs4233367	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4564157	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656993	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5082	0.81[GIH][hapmap]
rs7512012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic 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	119 gene(s)	inside rSNPs	diseases
2	esv32799	chr1:161161838-161171520	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4589131	B4GALT3	cis	cerebellum	SCAN
rs4589131	OR10J5	cis	cerebellum	SCAN
rs4589131	NES	cis	cerebellum	SCAN
rs4589131	FCRL3	cis	parietal	SCAN
rs4589131	DCAF8	cis	cerebellum	SCAN
rs4589131	TAGLN2	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161162800-161168400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:161163000-161168200	Weak transcription	Fetal Brain Male	brain
3	chr1:161163000-161169400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:161163200-161168000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:161165200-161168000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:161165200-161169600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:161165400-161167800	Weak transcription	Fetal Thymus	thymus
8	chr1:161165400-161168000	Active TSS	Right Atrium	heart
9	chr1:161165400-161168000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:161165400-161169200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr1:161165400-161169600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:161165600-161167800	Active TSS	Left Ventricle	heart
13	chr1:161165600-161170800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:161165800-161168800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:161165800-161168800	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr1:161165800-161169200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:161165800-161169400	Weak transcription	Primary T cells from cord blood	blood
18	chr1:161165800-161169800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:161166000-161168600	Active TSS	Pancreas	Pancrea
20	chr1:161166000-161168800	Active TSS	Psoas Muscle	Psoas
21	chr1:161166000-161169000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:161166000-161169200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr1:161166000-161169400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:161166000-161169600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:161166000-161170000	Weak transcription	GM12878-XiMat	blood
26	chr1:161166200-161167800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:161166200-161169000	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr1:161166200-161169400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:161166200-161169800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr1:161166200-161171800	Enhancers	Spleen	Spleen
31	chr1:161166400-161167800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr1:161166400-161167800	Active TSS	Placenta Amnion	Placenta Amnion
33	chr1:161166400-161168000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:161166400-161168000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:161166400-161168000	Active TSS	Gastric	stomach
36	chr1:161166400-161168400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
37	chr1:161166400-161168600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr1:161166400-161168800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr1:161166400-161168800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:161166400-161168800	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr1:161166400-161168800	Flanking Active TSS	Fetal Muscle Trunk	muscle
42	chr1:161166400-161168800	Flanking Active TSS	HSMM	muscle
43	chr1:161166400-161168800	Flanking Active TSS	HSMMtube	muscle
44	chr1:161166400-161169200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:161166400-161169200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr1:161166400-161169200	Enhancers	NH-A	brain
47	chr1:161166400-161169400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:161166400-161169600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:161166600-161168000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr1:161166600-161168400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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