Variant report

Variant	rs4687609
Chromosome Location	chr3:52140591-52140592
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52107340..52110604-chr3:52139807..52142191,3	K562	blood:
2	chr3:52133422..52135026-chr3:52139587..52141150,2	MCF-7	breast:
3	chr3:52119415..52123026-chr3:52140546..52143765,3	K562	blood:
4	chr3:52140403..52143176-chr3:52145230..52148198,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12485855	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12488456	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12489539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493204	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12496447	0.83[MEX][hapmap]
rs17051963	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2334960	1.00[YRI][hapmap]
rs2878438	0.83[MEX][hapmap]
rs3821841	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4687608	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4687801	0.85[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4687802	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687805	0.83[MEX][hapmap]
rs4687806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687808	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687810	0.83[MEX][hapmap]
rs66530305	0.81[AMR][1000 genomes]
rs6778442	0.83[MEX][hapmap]
rs72622937	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs731684	0.83[MEX][hapmap]
rs735768	0.83[MEX][hapmap]
rs747343	0.87[MEX][hapmap]
rs749995	0.83[MEX][hapmap]
rs7618573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs920160	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9637473	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9851576	0.83[MEX][hapmap]
rs9873175	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52105800-52142400	Weak transcription	Primary B cells from cord blood	blood
2	chr3:52110600-52179400	Weak transcription	Brain Germinal Matrix	brain
3	chr3:52122800-52142200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:52124200-52157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:52124800-52142000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:52125800-52142400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:52126200-52160600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:52128200-52140800	Weak transcription	Spleen	Spleen
9	chr3:52128400-52142200	Weak transcription	NHDF-Ad	bronchial
10	chr3:52128400-52142600	Weak transcription	NH-A	brain
11	chr3:52128600-52157000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:52129200-52155400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:52131600-52142800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:52132000-52140600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:52132200-52146800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:52132200-52155200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:52132400-52142600	Weak transcription	NHLF	lung
18	chr3:52132400-52143600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:52132600-52140600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:52133000-52142400	Weak transcription	Fetal Lung	lung
21	chr3:52133000-52142400	Weak transcription	K562	blood
22	chr3:52133200-52140600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:52133200-52141000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:52133200-52142600	Weak transcription	Lung	lung
25	chr3:52133200-52143600	Weak transcription	HUVEC	blood vessel
26	chr3:52133200-52162000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:52133400-52142800	Weak transcription	Pancreas	Pancrea
28	chr3:52133400-52143800	Weak transcription	Stomach Mucosa	stomach
29	chr3:52133400-52144600	Weak transcription	Gastric	stomach
30	chr3:52133400-52155000	Weak transcription	Osteobl	bone
31	chr3:52133600-52142400	Weak transcription	HepG2	liver
32	chr3:52135400-52140600	Weak transcription	Fetal Stomach	stomach
33	chr3:52135400-52140600	Weak transcription	Fetal Thymus	thymus
34	chr3:52135400-52142000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr3:52135400-52142600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:52135800-52142200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:52136200-52142000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:52136400-52142600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:52136600-52140600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:52136600-52153600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:52136800-52140600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:52136800-52142200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:52136800-52142600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:52136800-52143000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr3:52136800-52144200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:52136800-52154400	Weak transcription	Hela-S3	cervix
47	chr3:52136800-52155000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:52136800-52156000	Weak transcription	A549	lung
49	chr3:52136800-52187200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr3:52137000-52142200	Weak transcription	HSMM	muscle

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