Variant report

Variant	rs1873626
Chromosome Location	chr3:49675142-49675143
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49654340..49656120-chr3:49672426..49675250,2	K562	blood:
2	chr3:49673401..49676066-chr3:49680626..49682586,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1050088	0.86[JPT][hapmap]
rs1060962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10865955	0.86[JPT][hapmap]
rs11130199	0.86[JPT][hapmap]
rs11130212	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1131095	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11709525	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11710037	0.92[ASN][1000 genomes]
rs11711485	0.86[JPT][hapmap]
rs11718165	0.81[ASN][1000 genomes]
rs11720264	0.88[JPT][hapmap]
rs11917431	0.87[ASN][1000 genomes]
rs11919311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11921590	0.87[ASN][1000 genomes]
rs12489092	0.88[JPT][hapmap]
rs12490267	0.92[EUR][1000 genomes]
rs12497288	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13085791	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13316695	0.92[ASN][1000 genomes]
rs1352890	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1568661	0.86[JPT][hapmap]
rs1801143	0.86[JPT][hapmap]
rs1826347	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs1873625	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2005557	1.00[CEU][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2131104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2131109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2172252	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2329020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960548	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3197999	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34762726	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35007338	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35404120	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35701831	0.86[JPT][hapmap]
rs3811697	0.86[JPT][hapmap]
rs3870338	0.86[JPT][hapmap]
rs3924462	0.86[JPT][hapmap]
rs4283605	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4625	0.86[JPT][hapmap]
rs4855835	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855839	0.86[JPT][hapmap]
rs4855847	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4855859	0.86[JPT][hapmap]
rs4855864	0.86[JPT][hapmap]
rs4855881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4855883	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4855884	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6765869	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6766131	0.86[JPT][hapmap]
rs6767878	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6770670	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6782577	0.96[CEU][hapmap]
rs6803222	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7614725	0.87[ASN][1000 genomes]
rs7622302	0.86[JPT][hapmap]
rs7633271	0.88[JPT][hapmap]
rs7637999	0.86[JPT][hapmap]
rs885592	0.86[JPT][hapmap]
rs9812791	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9822268	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs9823546	0.81[ASN][1000 genomes]
rs9824092	0.92[ASN][1000 genomes]
rs9827021	0.88[JPT][hapmap]
rs9827708	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9833611	0.87[ASN][1000 genomes]
rs9836291	0.81[ASN][1000 genomes]
rs9837027	0.86[JPT][hapmap]
rs9837341	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9837520	0.87[ASN][1000 genomes]
rs9841110	0.88[JPT][hapmap]
rs9853683	0.86[JPT][hapmap]
rs9858280	0.86[JPT][hapmap]
rs9858542	0.81[ASN][1000 genomes]
rs9862080	0.92[ASN][1000 genomes]
rs9875617	0.86[JPT][hapmap]
rs9882740	1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv3812	chr3:49669773-49680587	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv3393809	chr3:49674632-49675278	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv3461854	chr3:49674716-49675243	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3461855	chr3:49674716-49675243	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49655600-49676200	Weak transcription	HepG2	liver
2	chr3:49657600-49685400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:49660800-49682600	Weak transcription	Liver	Liver
4	chr3:49661600-49692400	Weak transcription	Ovary	ovary
5	chr3:49661800-49682200	Weak transcription	Fetal Brain Male	brain
6	chr3:49662800-49685000	Weak transcription	Right Ventricle	heart
7	chr3:49663800-49679600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:49664200-49683200	Weak transcription	Pancreas	Pancrea
9	chr3:49664600-49680000	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:49667600-49679800	Weak transcription	Brain Germinal Matrix	brain
11	chr3:49669400-49692000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:49669600-49679400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:49669600-49679800	Weak transcription	Fetal Brain Female	brain
14	chr3:49669600-49680000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:49670000-49680000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:49672800-49676000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:49673400-49676000	Enhancers	K562	blood
18	chr3:49673400-49676200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:49673600-49675600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr3:49673800-49675600	Enhancers	Brain Angular Gyrus	brain
21	chr3:49673800-49676400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:49673800-49676600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:49673800-49676600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:49673800-49676800	Enhancers	NHEK	skin
25	chr3:49673800-49692400	Weak transcription	Gastric	stomach
26	chr3:49674000-49675400	Enhancers	Brain Anterior Caudate	brain
27	chr3:49674000-49676000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:49674000-49676000	Enhancers	Spleen	Spleen
29	chr3:49674000-49676200	Enhancers	Hela-S3	cervix
30	chr3:49674000-49676600	Enhancers	HMEC	breast
31	chr3:49674200-49676400	Enhancers	Placenta Amnion	Placenta Amnion
32	chr3:49674400-49676400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:49674400-49676400	Enhancers	Fetal Muscle Trunk	muscle
34	chr3:49674400-49676400	Enhancers	HSMMtube	muscle
35	chr3:49674400-49680000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:49674600-49677600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:49675000-49676400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:49675000-49676400	Enhancers	Placenta	Placenta
39	chr3:49675000-49679400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:49675000-49680400	Weak transcription	Brain Inferior Temporal Lobe	brain

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