Variant report

Variant	rs6734415
Chromosome Location	chr2:55563364-55563365
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10153861	1.00[EUR][1000 genomes]
rs10181997	1.00[EUR][1000 genomes]
rs10184362	1.00[EUR][1000 genomes]
rs10186158	1.00[EUR][1000 genomes]
rs10199332	1.00[EUR][1000 genomes]
rs10201075	1.00[EUR][1000 genomes]
rs10202943	1.00[EUR][1000 genomes]
rs10209908	1.00[EUR][1000 genomes]
rs10518764	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs13383527	1.00[EUR][1000 genomes]
rs13384739	1.00[EUR][1000 genomes]
rs13389151	1.00[EUR][1000 genomes]
rs13389799	1.00[EUR][1000 genomes]
rs13390100	1.00[EUR][1000 genomes]
rs13398447	1.00[EUR][1000 genomes]
rs13402277	1.00[EUR][1000 genomes]
rs13404740	1.00[EUR][1000 genomes]
rs13405460	1.00[EUR][1000 genomes]
rs13406929	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs13408706	1.00[EUR][1000 genomes]
rs13411077	1.00[EUR][1000 genomes]
rs13411257	1.00[EUR][1000 genomes]
rs13412682	1.00[EUR][1000 genomes]
rs13416519	1.00[EUR][1000 genomes]
rs13417988	1.00[EUR][1000 genomes]
rs13419337	1.00[EUR][1000 genomes]
rs13424499	1.00[EUR][1000 genomes]
rs13426160	1.00[EUR][1000 genomes]
rs13426766	1.00[EUR][1000 genomes]
rs13429863	1.00[EUR][1000 genomes]
rs17046801	1.00[ASW][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17046820	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs17046828	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17046829	0.95[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17046835	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17046837	1.00[EUR][1000 genomes]
rs17046881	1.00[EUR][1000 genomes]
rs17046896	1.00[EUR][1000 genomes]
rs17046898	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046954	1.00[EUR][1000 genomes]
rs17046959	1.00[EUR][1000 genomes]
rs17046963	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs17046964	0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs17264948	1.00[EUR][1000 genomes]
rs2043716	1.00[EUR][1000 genomes]
rs28434193	1.00[EUR][1000 genomes]
rs28498550	1.00[EUR][1000 genomes]
rs3861571	1.00[EUR][1000 genomes]
rs3975804	1.00[EUR][1000 genomes]
rs56201519	1.00[EUR][1000 genomes]
rs57623398	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59695161	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60920006	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545485	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6545486	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6704701	1.00[EUR][1000 genomes]
rs6707774	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6710128	1.00[EUR][1000 genomes]
rs6714932	1.00[EUR][1000 genomes]
rs6715991	1.00[EUR][1000 genomes]
rs6719677	1.00[EUR][1000 genomes]
rs6726757	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6729144	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6735009	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6738517	1.00[EUR][1000 genomes]
rs6741630	1.00[EUR][1000 genomes]
rs6748541	1.00[EUR][1000 genomes]
rs6754036	1.00[EUR][1000 genomes]
rs6758229	1.00[EUR][1000 genomes]
rs6759625	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6759763	1.00[EUR][1000 genomes]
rs6761771	1.00[EUR][1000 genomes]
rs72915982	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72915989	1.00[AMR][1000 genomes]
rs72915991	1.00[AMR][1000 genomes]
rs72918961	1.00[EUR][1000 genomes]
rs72918964	1.00[EUR][1000 genomes]
rs72918965	1.00[EUR][1000 genomes]
rs72918972	1.00[EUR][1000 genomes]
rs72918975	1.00[EUR][1000 genomes]
rs72923130	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72923156	1.00[EUR][1000 genomes]
rs72923157	1.00[EUR][1000 genomes]
rs72923183	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72923187	1.00[EUR][1000 genomes]
rs72923194	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72923197	1.00[EUR][1000 genomes]
rs72924917	1.00[EUR][1000 genomes]
rs72924922	1.00[EUR][1000 genomes]
rs72927340	1.00[EUR][1000 genomes]
rs72927384	1.00[EUR][1000 genomes]
rs72927388	1.00[EUR][1000 genomes]
rs72929306	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7561604	1.00[EUR][1000 genomes]
rs7562535	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7577510	1.00[EUR][1000 genomes]
rs7589558	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7594907	1.00[EUR][1000 genomes]
rs9309264	1.00[EUR][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	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv874158	chr2:55513738-55619923	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv457941	chr2:55517491-55585915	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv582030	chr2:55517491-55585915	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
3	chr2:55512400-55577400	Weak transcription	Right Ventricle	heart
4	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:55519800-55579000	Weak transcription	Primary B cells from cord blood	blood
6	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr2:55521400-55591000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr2:55523000-55584400	Weak transcription	Aorta	Aorta
9	chr2:55523200-55584800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr2:55523600-55600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:55534200-55589400	Weak transcription	Pancreas	Pancrea
12	chr2:55537800-55609400	Weak transcription	Lung	lung
13	chr2:55539200-55567800	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:55539200-55579000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:55539200-55579000	Weak transcription	NHEK	skin
16	chr2:55541400-55564600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr2:55541400-55584400	Weak transcription	Spleen	Spleen
18	chr2:55541800-55574800	Weak transcription	Ovary	ovary
19	chr2:55542400-55589800	Weak transcription	Fetal Intestine Large	intestine
20	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
21	chr2:55544200-55581800	Weak transcription	Left Ventricle	heart
22	chr2:55546200-55585000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:55546600-55579000	Weak transcription	K562	blood
24	chr2:55546800-55578800	Weak transcription	GM12878-XiMat	blood
25	chr2:55547400-55590600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr2:55548200-55585000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:55548600-55574800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:55548800-55570000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:55548800-55574800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:55551800-55577000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:55552600-55567000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:55553400-55564600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:55553400-55577200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:55554000-55565800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:55554600-55577200	Weak transcription	Placenta	Placenta
36	chr2:55554800-55584200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:55554800-55591600	Weak transcription	HSMMtube	muscle
38	chr2:55555000-55566600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:55555000-55566800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:55555000-55582200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:55555200-55563800	Weak transcription	Fetal Kidney	kidney
42	chr2:55555200-55569800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:55555200-55574400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:55555200-55578800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:55555400-55565400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr2:55555400-55565400	Weak transcription	Adipose Nuclei	Adipose
48	chr2:55555800-55570400	Weak transcription	Liver	Liver
49	chr2:55555800-55586000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:55556600-55579000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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