Variant report

Variant	rs4687810
Chromosome Location	chr3:52169095-52169096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52168617..52171249-chr3:52179854..52182353,2	K562	blood:
2	chr3:52164453..52167041-chr3:52169058..52171568,2	MCF-7	breast:
3	chr3:52167954..52170136-chr3:52176956..52178725,2	K562	blood:
4	chr3:52162996..52167625-chr3:52168207..52172862,5	K562	blood:
5	chr3:52168843..52170779-chr3:52171993..52173703,2	K562	blood:
6	chr3:52164710..52167219-chr3:52168743..52171613,3	K562	blood:
7	chr3:52038485..52040129-chr3:52168244..52170735,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12386365	0.87[AFR][1000 genomes]
rs12495536	0.82[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12496447	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12629791	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2334961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28387060	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28452586	0.81[AFR][1000 genomes]
rs2878438	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs352152	0.93[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687607	0.88[ASW][hapmap];0.93[CEU][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4687609	0.83[MEX][hapmap]
rs4687805	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	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6777340	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778442	0.94[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6786592	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs731684	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs735768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747343	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs749995	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616695	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7644325	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs876782	0.80[LWK][hapmap];0.90[YRI][hapmap]
rs893055	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9809254	0.90[YRI][hapmap]
rs9828327	1.00[CEU][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9843852	0.89[YRI][hapmap]
rs9846049	0.89[YRI][hapmap]
rs9851576	0.88[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9874939	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	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
2	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
3	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
4	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
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52110600-52179400	Weak transcription	Brain Germinal Matrix	brain
2	chr3:52136800-52187200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:52140400-52178200	Strong transcription	Dnd41	blood
4	chr3:52148600-52179800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:52155200-52180000	Weak transcription	Fetal Intestine Large	intestine
6	chr3:52155200-52187200	Weak transcription	Colonic Mucosa	Colon
7	chr3:52156200-52178000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:52156200-52187600	Weak transcription	Primary T cells from cord blood	blood
9	chr3:52156600-52177800	Weak transcription	Fetal Brain Female	brain
10	chr3:52157200-52171600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:52157200-52187600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:52157400-52178200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:52157400-52187200	Weak transcription	Fetal Kidney	kidney
14	chr3:52157600-52178600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:52157800-52170200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:52158600-52172000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:52159800-52169200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:52160200-52170200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:52160200-52179600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:52160600-52182600	Weak transcription	NHDF-Ad	bronchial
21	chr3:52160800-52169600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:52161200-52176400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:52161400-52169200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:52161400-52178000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:52162400-52184800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:52162600-52170200	Weak transcription	Spleen	Spleen
27	chr3:52162600-52170600	Weak transcription	Osteobl	bone
28	chr3:52162600-52171400	Weak transcription	Right Ventricle	heart
29	chr3:52162600-52172600	Weak transcription	Ovary	ovary
30	chr3:52162800-52169200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:52162800-52170200	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:52162800-52170200	Weak transcription	Right Atrium	heart
33	chr3:52162800-52170200	Weak transcription	HUVEC	blood vessel
34	chr3:52162800-52170600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:52162800-52173200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:52162800-52173400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:52162800-52176400	Weak transcription	Placenta	Placenta
38	chr3:52162800-52176400	Weak transcription	HMEC	breast
39	chr3:52162800-52179400	Weak transcription	A549	lung
40	chr3:52162800-52187000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr3:52162800-52187200	Weak transcription	NH-A	brain
42	chr3:52163000-52176600	Weak transcription	K562	blood
43	chr3:52163200-52177400	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr3:52163400-52173400	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:52163400-52185000	Strong transcription	Thymus	Thymus
46	chr3:52163600-52169400	Strong transcription	Fetal Stomach	stomach
47	chr3:52163600-52176600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:52164400-52169200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr3:52164400-52170400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr3:52164800-52169600	Weak transcription	Primary monocytes fromperipheralblood	blood

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