Variant report

Variant	rs1408841
Chromosome Location	chr1:197484871-197484872
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10158300	1.00[AMR][1000 genomes]
rs1024920	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1028785	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10494753	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10494759	1.00[CHB][hapmap];1.00[AMR][1000 genomes]
rs10737689	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10737690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10737691	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10754226	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs10801610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10801611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10801615	1.00[AMR][1000 genomes]
rs10922241	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10922245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12089070	1.00[JPT][hapmap]
rs1359458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1362940	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1421389	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1421396	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1421398	1.00[AMR][1000 genomes]
rs1558975	1.00[AMR][1000 genomes]
rs1570809	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1582409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841893	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1862011	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs1886627	1.00[AMR][1000 genomes]
rs1923757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1977330	1.00[AMR][1000 genomes]
rs2013617	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2146484	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2147771	1.00[AMR][1000 genomes]
rs3790737	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3902061	1.00[AMR][1000 genomes]
rs4244150	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4427436	1.00[AMR][1000 genomes]
rs4428919	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4477311	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4915243	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes]
rs4915547	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4915548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6428407	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6428408	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6428409	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6662893	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6676028	0.89[AFR][1000 genomes]
rs6678240	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6678776	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6685459	0.85[AFR][1000 genomes]
rs7515671	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7519686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7543631	1.00[AMR][1000 genomes]
rs7553327	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs942050	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs981520	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521647	chr1:197464448-197529218	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv4010	chr1:197471463-197511397	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197467200-197499000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:197478000-197541200	Weak transcription	Aorta	Aorta
3	chr1:197478600-197491200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:197480000-197489600	Weak transcription	Psoas Muscle	Psoas
5	chr1:197480000-197489800	Weak transcription	Brain Anterior Caudate	brain
6	chr1:197480000-197491000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:197480000-197535800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:197480200-197485400	Weak transcription	Thymus	Thymus
9	chr1:197480200-197485600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr1:197480200-197489200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:197480200-197541200	Weak transcription	Esophagus	oesophagus
12	chr1:197480200-197541200	Weak transcription	Fetal Thymus	thymus
13	chr1:197480400-197485800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:197480400-197487200	Weak transcription	Ovary	ovary
15	chr1:197480400-197541200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:197480600-197486800	Weak transcription	Fetal Brain Male	brain
17	chr1:197481000-197507000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:197481200-197485800	Weak transcription	Primary B cells from cord blood	blood
19	chr1:197481200-197491200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:197481200-197503400	Weak transcription	Primary T cells from cord blood	blood
21	chr1:197481200-197504200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:197481200-197507200	Weak transcription	Dnd41	blood
23	chr1:197481200-197508000	Weak transcription	Left Ventricle	heart
24	chr1:197481200-197513400	Weak transcription	Adipose Nuclei	Adipose
25	chr1:197481400-197487800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:197481400-197503600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:197481400-197529600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:197482000-197508000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:197482000-197508000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:197482200-197491000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:197482200-197495200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:197482200-197507600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:197482200-197507800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr1:197482600-197488200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr1:197484000-197487800	Enhancers	Fetal Lung	lung
36	chr1:197484600-197485000	Enhancers	Fetal Heart	heart
37	chr1:197484600-197485200	Enhancers	Duodenum Smooth Muscle	Duodenum

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