Variant report

Variant	rs867619
Chromosome Location	chr3:46537750-46537751
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:46537470-46537980	Hela-S3	cervix:	n/a	n/a
2	RCOR1	chr3:46537241-46539044	IMR90	lung:	n/a	n/a
3	JUND	chr3:46537536-46537910	SK-N-SH	brain:	n/a	n/a
4	RAD21	chr3:46537341-46537936	IMR90	lung:	n/a	n/a
5	CEBPB	chr3:46537310-46538028	IMR90	lung:	n/a	n/a
6	EP300	chr3:46537570-46537963	Hela-S3	cervix:	n/a	n/a
7	MAFK	chr3:46537443-46538006	IMR90	lung:	n/a	chr3:46537823-46537840
8	ZNF274	chr3:46537658-46538225	K562	blood:	n/a	n/a
9	TCF12	chr3:46537546-46538098	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr3:46537442-46538170	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46537655..46538429-chr3:46599459..46599986,2	MCF-7	breast:

Variant related genes	Relation type
RTP3	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10865942	0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs17078863	1.00[CEU][hapmap]
rs17078878	1.00[CEU][hapmap]
rs1814973	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1879328	1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2888531	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34334514	0.96[EUR][1000 genomes]
rs34504121	0.89[EUR][1000 genomes]
rs35714147	0.91[EUR][1000 genomes]
rs4521278	1.00[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs4683235	1.00[CEU][hapmap]
rs4683241	1.00[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4683242	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683243	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55786118	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59244195	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60983021	0.96[EUR][1000 genomes]
rs6442000	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67227548	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6774189	0.94[GIH][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs6776621	1.00[CEU][hapmap]
rs6791941	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6804045	0.88[ASN][1000 genomes]
rs72622927	0.83[ASN][1000 genomes]
rs72900270	0.89[EUR][1000 genomes]
rs72900281	0.96[EUR][1000 genomes]
rs7428292	0.89[EUR][1000 genomes]
rs7629657	1.00[CEU][hapmap]
rs7643332	0.96[EUR][1000 genomes]
rs883738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883740	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014624	chr3:46463424-46549188	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1009892	chr3:46496775-46546918	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv536553	chr3:46496775-46546918	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46530800-46538600	Weak transcription	Pancreas	Pancrea
2	chr3:46531000-46538400	Weak transcription	Lung	lung
3	chr3:46531200-46541600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:46531400-46540200	Weak transcription	Left Ventricle	heart
5	chr3:46532400-46538400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:46532400-46538400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:46532800-46538000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:46533000-46538400	Weak transcription	Right Ventricle	heart
9	chr3:46533000-46544200	Weak transcription	Psoas Muscle	Psoas
10	chr3:46534600-46538400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:46535000-46538600	Weak transcription	Fetal Intestine Large	intestine
12	chr3:46537200-46537800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:46537200-46538000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:46537200-46538200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:46537200-46538200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr3:46537200-46538200	Enhancers	HMEC	breast
17	chr3:46537200-46538200	Enhancers	HSMM	muscle
18	chr3:46537200-46538200	Enhancers	HSMMtube	muscle
19	chr3:46537200-46538200	Enhancers	NHEK	skin
20	chr3:46537200-46538200	Enhancers	NHLF	lung
21	chr3:46537200-46538400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:46537200-46538400	Enhancers	Liver	Liver
23	chr3:46537200-46538400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr3:46537200-46538600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr3:46537200-46538600	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr3:46537200-46538600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:46537200-46538600	Enhancers	NH-A	brain
28	chr3:46537200-46538600	Enhancers	NHDF-Ad	bronchial
29	chr3:46537200-46538800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr3:46537200-46538800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:46537200-46538800	Enhancers	Osteobl	bone
32	chr3:46537200-46539000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr3:46537200-46539000	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr3:46537200-46539200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:46537200-46540000	Enhancers	Dnd41	blood
36	chr3:46537200-46546200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:46537200-46547000	Enhancers	Fetal Thymus	thymus
38	chr3:46537200-46550200	Enhancers	K562	blood
39	chr3:46537400-46537800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr3:46537400-46537800	Enhancers	Fetal Stomach	stomach
41	chr3:46537400-46537800	Enhancers	Hela-S3	cervix
42	chr3:46537400-46538200	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr3:46537400-46538200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:46537400-46538200	Enhancers	Colon Smooth Muscle	Colon
45	chr3:46537400-46538200	Enhancers	Stomach Smooth Muscle	stomach
46	chr3:46537400-46538800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:46537400-46539000	Enhancers	HUVEC	blood vessel
48	chr3:46537400-46539600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:46537400-46542000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:46537600-46538200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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