Variant report

Variant	rs13398447
Chromosome Location	chr2:55531238-55531239
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10153861	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10181997	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10184362	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10186158	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10191785	0.93[AFR][1000 genomes]
rs10194658	0.95[AFR][1000 genomes]
rs10196295	0.92[AFR][1000 genomes]
rs10199332	1.00[EUR][1000 genomes]
rs10201075	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10202943	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10209908	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10518764	0.84[AFR][1000 genomes]
rs13383527	1.00[EUR][1000 genomes]
rs13384739	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13389151	1.00[EUR][1000 genomes]
rs13389799	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13390100	1.00[EUR][1000 genomes]
rs13402277	1.00[EUR][1000 genomes]
rs13404740	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13405460	1.00[EUR][1000 genomes]
rs13406929	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13408706	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13411077	1.00[EUR][1000 genomes]
rs13411257	1.00[EUR][1000 genomes]
rs13412682	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13416519	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13417988	1.00[EUR][1000 genomes]
rs13419337	1.00[EUR][1000 genomes]
rs13424499	1.00[EUR][1000 genomes]
rs13426160	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13426766	1.00[EUR][1000 genomes]
rs13429863	1.00[EUR][1000 genomes]
rs17046801	1.00[EUR][1000 genomes]
rs17046820	1.00[EUR][1000 genomes]
rs17046828	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17046829	1.00[EUR][1000 genomes]
rs17046835	1.00[EUR][1000 genomes]
rs17046837	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046881	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17046896	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17046898	1.00[EUR][1000 genomes]
rs17046954	1.00[EUR][1000 genomes]
rs17046959	1.00[EUR][1000 genomes]
rs17046963	1.00[EUR][1000 genomes]
rs17046964	1.00[EUR][1000 genomes]
rs17264948	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2043716	1.00[EUR][1000 genomes]
rs28434193	0.86[AFR][1000 genomes];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	1.00[EUR][1000 genomes]
rs59695161	1.00[EUR][1000 genomes]
rs60920006	1.00[EUR][1000 genomes]
rs6545485	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6545486	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6704701	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6707774	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6710128	1.00[EUR][1000 genomes]
rs6714932	1.00[EUR][1000 genomes]
rs6715991	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6717221	0.89[AMR][1000 genomes]
rs6719677	1.00[EUR][1000 genomes]
rs6726757	1.00[EUR][1000 genomes]
rs6729144	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6734415	1.00[EUR][1000 genomes]
rs6735009	1.00[EUR][1000 genomes]
rs6738517	1.00[EUR][1000 genomes]
rs6741630	1.00[EUR][1000 genomes]
rs6746757	0.93[AFR][1000 genomes]
rs6746983	0.93[AFR][1000 genomes]
rs6747974	0.93[AFR][1000 genomes]
rs6748541	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6754036	1.00[EUR][1000 genomes]
rs6758229	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6759625	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6759763	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6759957	0.94[AFR][1000 genomes]
rs6761771	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918961	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918964	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918965	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918972	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72918975	1.00[EUR][1000 genomes]
rs72923130	1.00[EUR][1000 genomes]
rs72923156	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923157	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923183	1.00[EUR][1000 genomes]
rs72923187	1.00[EUR][1000 genomes]
rs72923194	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	1.00[EUR][1000 genomes]
rs7561604	1.00[EUR][1000 genomes]
rs7562535	1.00[EUR][1000 genomes]
rs7577510	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7589558	1.00[EUR][1000 genomes]
rs7594907	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9309264	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55509000-55541200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55509400-55545200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:55510000-55541600	Weak transcription	Esophagus	oesophagus
4	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55510200-55542200	Weak transcription	Fetal Intestine Large	intestine
7	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
8	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
9	chr2:55510600-55533800	Weak transcription	Pancreas	Pancrea
10	chr2:55510600-55536600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:55510600-55537400	Weak transcription	Lung	lung
12	chr2:55510800-55542200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:55511000-55540600	Weak transcription	Spleen	Spleen
14	chr2:55511200-55542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:55511200-55547000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:55512000-55549800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:55512400-55577400	Weak transcription	Right Ventricle	heart
18	chr2:55512600-55546000	Weak transcription	Small Intestine	intestine
19	chr2:55513600-55531400	Strong transcription	Dnd41	blood
20	chr2:55514800-55549600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:55515800-55550400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:55518600-55532200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:55519400-55533400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:55519800-55579000	Weak transcription	Primary B cells from cord blood	blood
26	chr2:55520000-55538800	Weak transcription	Ovary	ovary
27	chr2:55520000-55541200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:55520200-55531600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:55520200-55539000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr2:55520200-55554400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr2:55521400-55591000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr2:55521800-55531600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr2:55523000-55534800	Weak transcription	Primary T cells from cord blood	blood
35	chr2:55523000-55534800	Weak transcription	Liver	Liver
36	chr2:55523000-55537400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:55523000-55538800	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:55523000-55548000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:55523000-55584400	Weak transcription	Aorta	Aorta
40	chr2:55523200-55537800	Weak transcription	HSMMtube	muscle
41	chr2:55523200-55584800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:55523600-55533800	Weak transcription	NHLF	lung
43	chr2:55523600-55534400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:55523600-55535800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:55523600-55537400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:55523600-55537800	Weak transcription	Fetal Heart	heart
47	chr2:55523600-55541000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:55523600-55542000	Weak transcription	Fetal Brain Male	brain
49	chr2:55523600-55548000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:55523600-55600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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