Variant report

Variant	rs6717048
Chromosome Location	chr2:233586427-233586428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10210953	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1022329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427328	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1078323	0.96[CEU][hapmap]
rs1083522	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs10933406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1104764	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11688166	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs11689851	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs11893358	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12105766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12619195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12999865	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13007579	0.93[CEU][hapmap]
rs13024330	0.92[CEU][hapmap]
rs13029336	0.83[JPT][hapmap]
rs1515961	0.83[JPT][hapmap]
rs17164	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs1973675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012423	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2289911	0.93[CEU][hapmap]
rs2293780	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2344611	0.88[EUR][1000 genomes]
rs2344613	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs2592104	0.82[EUR][1000 genomes]
rs2675954	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2675968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs283470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs283473	0.83[JPT][hapmap]
rs283487	0.83[EUR][1000 genomes]
rs4144795	0.83[EUR][1000 genomes]
rs4144797	0.82[EUR][1000 genomes]
rs4973563	0.93[CEU][hapmap]
rs4973564	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs62193269	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62193271	0.87[EUR][1000 genomes]
rs6704763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6710294	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6716488	0.87[EUR][1000 genomes]
rs6733495	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6739794	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs709937	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs737027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs748002	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs778341	0.95[YRI][hapmap]
rs778370	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs921055	0.92[CEU][hapmap]
rs938569	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs974321	0.83[EUR][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	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233564000-233589000	Weak transcription	NH-A	brain
2	chr2:233564200-233596400	Weak transcription	NHLF	lung
3	chr2:233564200-233613000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:233564800-233592800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:233565000-233612200	Weak transcription	Fetal Brain Male	brain
6	chr2:233565200-233589800	Weak transcription	HMEC	breast
7	chr2:233565200-233602000	Weak transcription	HUVEC	blood vessel
8	chr2:233565200-233606400	Weak transcription	Stomach Mucosa	stomach
9	chr2:233565400-233589800	Weak transcription	Hela-S3	cervix
10	chr2:233565400-233590000	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:233566800-233612800	Weak transcription	Small Intestine	intestine
13	chr2:233568000-233604400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr2:233569200-233589000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:233569200-233590000	Weak transcription	NHDF-Ad	bronchial
16	chr2:233569200-233615000	Weak transcription	Colonic Mucosa	Colon
17	chr2:233569400-233612800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:233569400-233615400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:233570600-233593400	Weak transcription	Aorta	Aorta
20	chr2:233571200-233593600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:233571200-233598200	Weak transcription	Fetal Kidney	kidney
22	chr2:233571200-233627400	Weak transcription	Gastric	stomach
23	chr2:233571400-233588600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:233571400-233601800	Weak transcription	Esophagus	oesophagus
25	chr2:233571600-233612200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:233572200-233589000	Weak transcription	Osteobl	bone
27	chr2:233572200-233589800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr2:233572200-233589800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:233572200-233591600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:233572200-233593200	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:233572400-233586800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:233573600-233589800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:233573800-233588600	Weak transcription	Lung	lung
34	chr2:233574200-233588800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:233574200-233589000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:233574200-233589200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr2:233574400-233588200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:233574400-233593400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:233575400-233586800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:233576000-233589000	Weak transcription	Brain Germinal Matrix	brain
41	chr2:233577400-233589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:233580000-233606000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:233580200-233589400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:233580200-233596000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr2:233580600-233604000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:233580800-233595200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:233581000-233594200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:233581200-233587600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr2:233581400-233589000	Weak transcription	Brain Angular Gyrus	brain
50	chr2:233581400-233589000	Weak transcription	Pancreas	Pancrea

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