Variant report

Variant	rs4687805
Chromosome Location	chr3:52123313-52123314
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52123230..52125073-chr3:52183887..52186377,2	MCF-7	breast:
2	chr3:52105087..52107188-chr3:52123209..52125122,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12495536	0.88[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12496447	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12629791	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13316105	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2334961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28387060	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2878438	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs352152	0.93[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687607	0.94[ASW][hapmap];0.93[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4687609	0.83[MEX][hapmap]
rs4687810	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6773704	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6777340	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6778442	0.87[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6786592	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs731684	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs735768	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs747343	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs749995	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7616695	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7644325	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs876782	0.85[LWK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs893055	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9809254	0.85[LWK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs9828327	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9843852	0.93[YRI][hapmap]
rs9846049	0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs9851576	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9874939	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52103200-52124800	Weak transcription	Colonic Mucosa	Colon
2	chr3:52105600-52124000	Weak transcription	Pancreas	Pancrea
3	chr3:52105800-52124000	Weak transcription	Hela-S3	cervix
4	chr3:52105800-52142400	Weak transcription	Primary B cells from cord blood	blood
5	chr3:52109600-52123800	Weak transcription	NHEK	skin
6	chr3:52109600-52129800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:52110000-52125000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:52110000-52126000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:52110000-52126000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:52110000-52127000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:52110000-52127200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:52110000-52127400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:52110200-52125400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:52110600-52179400	Weak transcription	Brain Germinal Matrix	brain
15	chr3:52111200-52127000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:52115800-52133000	Weak transcription	Gastric	stomach
17	chr3:52118800-52124800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:52119000-52123600	Enhancers	Fetal Thymus	thymus
19	chr3:52119000-52124600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:52119200-52126800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:52119200-52127200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr3:52119200-52128400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr3:52119200-52128600	Enhancers	Fetal Muscle Trunk	muscle
24	chr3:52119600-52124800	Enhancers	Primary hematopoietic stem cells	blood
25	chr3:52119600-52129000	Enhancers	Fetal Muscle Leg	muscle
26	chr3:52119800-52123600	Enhancers	Spleen	Spleen
27	chr3:52119800-52124200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:52120000-52125400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:52120200-52124800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr3:52120600-52123800	Enhancers	Right Ventricle	heart
31	chr3:52120600-52124000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:52120600-52125000	Enhancers	HepG2	liver
33	chr3:52120600-52125400	Enhancers	HUVEC	blood vessel
34	chr3:52120600-52126200	Enhancers	Adipose Nuclei	Adipose
35	chr3:52120600-52126600	Enhancers	Left Ventricle	heart
36	chr3:52120600-52128800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:52120600-52128800	Enhancers	Placenta	Placenta
38	chr3:52120600-52129200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:52120800-52124200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:52120800-52124800	Enhancers	Fetal Stomach	stomach
41	chr3:52120800-52125400	Enhancers	Fetal Intestine Large	intestine
42	chr3:52120800-52125800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr3:52120800-52125800	Enhancers	K562	blood
44	chr3:52120800-52127400	Enhancers	Right Atrium	heart
45	chr3:52121000-52123600	Enhancers	HSMM	muscle
46	chr3:52121000-52123800	Enhancers	NH-A	brain
47	chr3:52121000-52124000	Enhancers	Muscle Satellite Cultured Cells	--
48	chr3:52121000-52126200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:52121000-52128400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:52121000-52128400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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