Variant report

Variant	rs17045292
Chromosome Location	chr2:54050281-54050282
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10185375	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10190578	0.82[CHB][hapmap]
rs10210726	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs10490470	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs12162342	0.84[EUR][1000 genomes]
rs12612589	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12613682	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs12616124	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12616774	0.83[CHB][hapmap]
rs12617360	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs12617668	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12618276	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12618587	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12618833	0.85[JPT][hapmap]
rs12620190	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12620208	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12621557	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12621635	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12623380	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs13393197	0.81[ASN][1000 genomes]
rs13414183	0.82[CHB][hapmap]
rs13414472	0.83[CHB][hapmap]
rs13415842	0.89[AMR][1000 genomes]
rs17045125	0.82[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs17045215	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17045370	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs17045386	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs17045435	0.87[CEU][hapmap]
rs2009149	0.89[AMR][1000 genomes]
rs2272249	0.92[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2272250	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2287344	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2287345	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2357491	0.85[CEU][hapmap]
rs28439002	0.84[ASN][1000 genomes]
rs3213775	0.87[CEU][hapmap]
rs3731972	0.87[CEU][hapmap]
rs3770389	0.87[EUR][1000 genomes]
rs3770400	0.83[CHB][hapmap]
rs3770401	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs3770415	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs3821078	0.87[EUR][1000 genomes]
rs3821080	0.82[CHB][hapmap]
rs3850347	1.00[CEU][hapmap]
rs3861570	0.85[ASN][1000 genomes]
rs55839073	0.81[ASN][1000 genomes]
rs6712204	0.82[CHB][hapmap]
rs6714424	0.82[CHB][hapmap]
rs72799229	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72799234	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72799235	0.83[ASN][1000 genomes]
rs72799236	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72799239	0.87[EUR][1000 genomes]
rs72799259	0.84[EUR][1000 genomes]
rs7568771	0.81[ASN][1000 genomes]
rs7586686	0.82[CHB][hapmap]
rs7595713	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs7600276	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7609067	0.83[CHB][hapmap]
rs805371	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54015200-54051600	Weak transcription	Stomach Mucosa	stomach
2	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:54015800-54054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:54023000-54053800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:54025800-54062000	Weak transcription	Right Ventricle	heart
7	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:54030400-54063000	Weak transcription	Esophagus	oesophagus
9	chr2:54035800-54052800	Weak transcription	Brain Substantia Nigra	brain
10	chr2:54038800-54053000	Weak transcription	Fetal Brain Male	brain
11	chr2:54040200-54055000	Weak transcription	Fetal Heart	heart
12	chr2:54040600-54053000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:54040800-54053000	Weak transcription	Brain Angular Gyrus	brain
14	chr2:54040800-54053000	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:54041400-54054600	Weak transcription	Psoas Muscle	Psoas
16	chr2:54041400-54056400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:54042800-54062200	Weak transcription	Fetal Kidney	kidney
18	chr2:54043000-54053800	Weak transcription	NHEK	skin
19	chr2:54043200-54053000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:54043200-54053800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:54043400-54053000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:54043400-54053600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:54045400-54053000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:54045400-54053000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:54046000-54053600	Weak transcription	NH-A	brain
26	chr2:54046200-54050600	Strong transcription	Fetal Stomach	stomach
27	chr2:54046400-54053000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:54046600-54080200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:54046600-54080200	Weak transcription	NHDF-Ad	bronchial
30	chr2:54046800-54053000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:54046800-54054000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:54046800-54054200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:54046800-54054200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:54046800-54056800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:54046800-54060400	Weak transcription	Primary B cells from cord blood	blood
36	chr2:54046800-54070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:54046800-54080400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:54047000-54051200	Weak transcription	HUVEC	blood vessel
39	chr2:54047000-54053000	Weak transcription	Ovary	ovary
40	chr2:54047000-54053000	Weak transcription	HMEC	breast
41	chr2:54047000-54053800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:54047000-54054000	Weak transcription	NHLF	lung
43	chr2:54047000-54056600	Weak transcription	Brain Germinal Matrix	brain
44	chr2:54047000-54060600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr2:54047000-54061400	Weak transcription	Fetal Thymus	thymus
46	chr2:54047000-54080200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:54047000-54080200	Weak transcription	A549	lung
48	chr2:54047000-54080400	Weak transcription	Gastric	stomach
49	chr2:54047000-54080400	Weak transcription	Pancreas	Pancrea
50	chr2:54047000-54080800	Weak transcription	Aorta	Aorta

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