Variant report

Variant	rs1488189
Chromosome Location	chr3:112711371-112711372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr3:112711264-112711558	K562	blood:	n/a	n/a
2	MXI1	chr3:112711287-112711396	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:112358718..112361602-chr3:112709202..112711684,5	MCF-7	breast:
2	chr3:112709917..112711539-chr3:113232036..113234156,2	K562	blood:
3	chr3:112357488..112363507-chr3:112707947..112711649,7	K562	blood:
4	chr3:112710705..112712434-chr3:112736471..112738011,2	K562	blood:
5	chr3:112709706..112712038-chr3:112736780..112739124,2	MCF-7	breast:
6	chr3:112709836..112712161-chr3:112728676..112730465,2	MCF-7	breast:
7	chr3:112358506..112363260-chr3:112706755..112711649,8	K562	blood:
8	chr3:112709111..112712767-chr3:112725826..112728376,3	K562	blood:
9	chr3:112708671..112711453-chr3:112735992..112738475,2	K562	blood:
10	chr3:112279683..112282381-chr3:112710182..112712390,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272844	TF binding region
ENSG00000163611	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000138459	Chromatin interaction
ENSG00000240057	Chromatin interaction
ENSG00000163608	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10934211	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11718449	1.00[MEX][hapmap];0.82[TSI][hapmap]
rs1488190	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2272393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293560	0.93[ASN][1000 genomes]
rs2293562	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2306857	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33940464	0.83[YRI][hapmap]
rs3872610	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs3889123	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682451	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4682452	1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6438123	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs6796453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7633507	0.94[ASN][1000 genomes]
rs7650656	1.00[MEX][hapmap];0.82[TSI][hapmap]
rs9288967	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9866791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9874803	0.83[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv1843165	chr3:112628205-112740145	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription 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 target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1488189	C3orf17	cis	cerebellum	SCAN
rs1488189	GTPBP8	cis	lymphoblastoid	seeQTL
rs1488189	SIDT1	cis	cerebellum	SCAN
rs1488189	GTPBP8	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112709000-112711600	Active TSS	K562	blood
2	chr3:112709200-112711600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr3:112709200-112711800	Active TSS	NHLF	lung
4	chr3:112709400-112711400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:112709400-112711400	Active TSS	Thymus	Thymus
6	chr3:112709400-112711600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:112709400-112711800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:112709400-112712000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:112709600-112711400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:112709600-112711600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:112709600-112711600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:112710400-112711400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:112710400-112711400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:112710400-112711600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr3:112710400-112712400	Weak transcription	Gastric	stomach
16	chr3:112710400-112721200	Weak transcription	Lung	lung
17	chr3:112710400-112721400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:112710400-112721400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:112710400-112724200	Weak transcription	Small Intestine	intestine
20	chr3:112710400-112737400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:112710600-112711400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:112710600-112711400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr3:112710600-112711400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr3:112710600-112711400	Flanking Active TSS	Liver	Liver
25	chr3:112710600-112711400	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr3:112710600-112711400	Flanking Active TSS	NH-A	brain
27	chr3:112710600-112711600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:112710600-112711600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:112710600-112711600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr3:112710600-112711800	Flanking Active TSS	Fetal Brain Male	brain
31	chr3:112710600-112712000	Flanking Active TSS	Dnd41	blood
32	chr3:112710600-112712400	Weak transcription	Aorta	Aorta
33	chr3:112710600-112712600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr3:112710600-112712800	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr3:112710600-112715800	Weak transcription	Placenta	Placenta
36	chr3:112710600-112716800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:112710600-112717000	Weak transcription	Esophagus	oesophagus
38	chr3:112710600-112717000	Weak transcription	Left Ventricle	heart
39	chr3:112710600-112721000	Weak transcription	Pancreas	Pancrea
40	chr3:112710600-112721000	Weak transcription	Right Ventricle	heart
41	chr3:112710600-112721000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:112710600-112721200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:112710600-112721200	Weak transcription	Ovary	ovary
44	chr3:112710600-112721400	Weak transcription	HSMMtube	muscle
45	chr3:112710600-112723800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:112710600-112725000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr3:112710800-112711400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:112710800-112711400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr3:112710800-112711400	Enhancers	Primary B cells from peripheral blood	blood
50	chr3:112710800-112711400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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