Variant report

Variant	rs1828398
Chromosome Location	chr2:63034870-63034871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10153716	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1022110	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11682530	0.92[CEU][hapmap];0.92[YRI][hapmap];0.86[EUR][1000 genomes]
rs11688816	0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs11893131	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713467	0.83[EUR][1000 genomes]
rs12713468	0.92[CEU][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12989754	0.96[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12994674	0.89[AFR][1000 genomes]
rs13013218	0.96[CEU][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13398408	0.83[YRI][hapmap]
rs13410889	0.83[CHB][hapmap]
rs13418889	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1420018	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs1468748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1553832	0.92[CEU][hapmap];0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17027429	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1877026	0.83[CHB][hapmap]
rs189671	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1906198	0.88[CEU][hapmap]
rs2058566	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2058567	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2080227	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2136737	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2215870	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs2421816	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2430388	0.96[CEU][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes]
rs2539978	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2539980	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2539984	0.86[ASN][1000 genomes]
rs2539985	0.85[EUR][1000 genomes]
rs2539987	0.96[CEU][hapmap];0.83[YRI][hapmap]
rs2710637	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2710639	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2710640	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2710642	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs34104251	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360797	0.84[CEU][hapmap];0.83[YRI][hapmap]
rs360799	0.87[CEU][hapmap]
rs360800	0.88[CEU][hapmap]
rs360801	0.84[CEU][hapmap]
rs360804	0.88[CEU][hapmap]
rs360807	0.92[CEU][hapmap];0.83[YRI][hapmap]
rs3927201	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4461246	0.96[CEU][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4671050	0.96[CEU][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4671051	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4671450	0.82[EUR][1000 genomes]
rs6545971	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6545972	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545973	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6714241	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7557501	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7562149	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7562734	0.92[EUR][1000 genomes]
rs7567923	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7571916	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7573756	0.92[CEU][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7591708	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs9678329	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9789661	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9973612	0.96[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv428041	chr2:63027947-63206574	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63017000-63037400	Weak transcription	NHLF	lung
2	chr2:63017400-63049400	Weak transcription	Fetal Heart	heart
3	chr2:63019600-63043400	Weak transcription	Brain Angular Gyrus	brain
4	chr2:63020600-63082000	Weak transcription	Pancreas	Pancrea
5	chr2:63020800-63040200	Weak transcription	Left Ventricle	heart
6	chr2:63022400-63040400	Weak transcription	NHEK	skin
7	chr2:63022400-63041000	Weak transcription	HSMM	muscle
8	chr2:63022800-63035800	Weak transcription	Fetal Kidney	kidney
9	chr2:63023800-63049000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:63028000-63037600	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:63028600-63063400	Weak transcription	Brain Substantia Nigra	brain
12	chr2:63029600-63040600	Weak transcription	HMEC	breast
13	chr2:63031000-63083000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:63031400-63082000	Weak transcription	Thymus	Thymus
15	chr2:63031600-63040800	Weak transcription	NH-A	brain
16	chr2:63031600-63053800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr2:63031800-63035600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:63032000-63035400	Strong transcription	NHDF-Ad	bronchial
19	chr2:63032000-63040200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:63032600-63036600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:63032800-63035200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:63032800-63036000	ZNF genes & repeats	Dnd41	blood
23	chr2:63033000-63037400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:63033200-63035200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:63033400-63035200	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:63033400-63035200	ZNF genes & repeats	Fetal Stomach	stomach
27	chr2:63033400-63035400	ZNF genes & repeats	Fetal Intestine Large	intestine
28	chr2:63033400-63035400	ZNF genes & repeats	Fetal Intestine Small	intestine
29	chr2:63033400-63040200	Weak transcription	Esophagus	oesophagus
30	chr2:63033600-63035000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:63033800-63035200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:63033800-63035400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:63033800-63039000	Weak transcription	Ovary	ovary
34	chr2:63033800-63040200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:63033800-63040200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:63033800-63040400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:63033800-63040600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:63033800-63052800	Weak transcription	Primary T cells from cord blood	blood
39	chr2:63033800-63060600	Weak transcription	Aorta	Aorta
40	chr2:63034000-63035600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:63034000-63040200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr2:63034200-63036400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:63034200-63037400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:63034200-63037400	Weak transcription	HepG2	liver
45	chr2:63034200-63038800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:63034400-63036000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:63034400-63037600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr2:63034400-63037600	Weak transcription	Osteobl	bone
49	chr2:63034400-63040000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:63034400-63040200	Weak transcription	A549	lung

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