Variant report

Variant	rs6778442
Chromosome Location	chr3:52148483-52148484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52142908..52145897-chr3:52147537..52149613,3	K562	blood:
2	chr3:52148055..52150067-chr3:52157333..52159014,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12495536	0.93[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12496447	0.87[ASW][hapmap];0.93[CEU][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12629791	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2334961	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28387060	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2878438	0.87[ASW][hapmap];0.93[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs352152	0.87[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4687607	0.81[ASW][hapmap];0.87[CEU][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4687609	0.83[MEX][hapmap]
rs4687805	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]
rs4687810	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]
rs6773704	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6777340	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6786592	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs731684	0.87[ASW][hapmap];0.93[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs735768	0.94[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs747343	0.87[ASW][hapmap];0.93[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs749995	0.94[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7616695	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7644325	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs876782	0.86[YRI][hapmap]
rs893055	0.88[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9809254	0.86[YRI][hapmap]
rs9828327	0.93[CEU][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9851576	0.81[ASW][hapmap];0.93[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9874939	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[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	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	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
3	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
4	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
5	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
6	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
7	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

No data

Chromatin state (count:83 , 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	chr3:52124200-52157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:52126200-52160600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:52128600-52157000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:52129200-52155400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:52132200-52155200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:52133200-52162000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:52133400-52155000	Weak transcription	Osteobl	bone
9	chr3:52136600-52153600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:52136800-52154400	Weak transcription	Hela-S3	cervix
11	chr3:52136800-52155000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:52136800-52156000	Weak transcription	A549	lung
13	chr3:52136800-52187200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:52137200-52152400	Weak transcription	GM12878-XiMat	blood
15	chr3:52138200-52153800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:52138800-52149400	Strong transcription	Thymus	Thymus
17	chr3:52139600-52151400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:52139600-52154600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:52139800-52153800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:52140400-52178200	Strong transcription	Dnd41	blood
21	chr3:52140600-52160800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:52140800-52155000	Weak transcription	Primary T cells from cord blood	blood
23	chr3:52141400-52151400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:52141400-52154800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:52142200-52148600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:52142400-52148600	Weak transcription	HMEC	breast
27	chr3:52142800-52148800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:52143000-52151800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:52143000-52153800	Weak transcription	K562	blood
30	chr3:52143000-52154000	Weak transcription	NHLF	lung
31	chr3:52143000-52155000	Weak transcription	NH-A	brain
32	chr3:52143000-52156000	Weak transcription	Liver	Liver
33	chr3:52143200-52151400	Weak transcription	Brain Substantia Nigra	brain
34	chr3:52143200-52153200	Weak transcription	Placenta	Placenta
35	chr3:52143200-52154600	Weak transcription	NHDF-Ad	bronchial
36	chr3:52143200-52156000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:52143400-52155400	Weak transcription	HSMM	muscle
38	chr3:52144200-52152800	Weak transcription	Spleen	Spleen
39	chr3:52144200-52154600	Strong transcription	Fetal Stomach	stomach
40	chr3:52144200-52155000	Weak transcription	Stomach Mucosa	stomach
41	chr3:52144200-52155200	Weak transcription	HUVEC	blood vessel
42	chr3:52144200-52163600	Weak transcription	Aorta	Aorta
43	chr3:52144400-52149000	Strong transcription	Fetal Thymus	thymus
44	chr3:52144400-52150400	Weak transcription	Brain Angular Gyrus	brain
45	chr3:52144400-52154400	Weak transcription	Fetal Intestine Large	intestine
46	chr3:52144600-52150400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:52144800-52148600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:52144800-52149000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:52145000-52150200	Weak transcription	Fetal Lung	lung
50	chr3:52145000-52154600	Weak transcription	Lung	lung

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