Variant report

Variant	rs1972340
Chromosome Location	chr1:171880715-171880716
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1015008	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1022541	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1040517	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10737337	0.81[ASN][1000 genomes]
rs10737338	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10753202	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10753203	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10753204	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10753205	0.82[ASN][1000 genomes]
rs1076700	0.82[ASN][1000 genomes]
rs10798695	0.82[ASN][1000 genomes]
rs10798701	0.82[ASN][1000 genomes]
rs10798702	0.82[ASN][1000 genomes]
rs10798705	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10798716	0.82[ASN][1000 genomes]
rs10798722	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10798725	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10798726	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913908	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1118173	0.82[ASN][1000 genomes]
rs12021814	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12024869	0.87[EUR][1000 genomes]
rs12025243	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12029015	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12040254	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12047542	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12405583	0.82[ASN][1000 genomes]
rs12747663	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1535301	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1555100	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1980488	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2145383	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2206543	0.82[ASN][1000 genomes]
rs2235696	0.82[ASN][1000 genomes]
rs2421915	0.82[ASN][1000 genomes]
rs2421947	0.82[ASN][1000 genomes]
rs2901600	0.82[ASN][1000 genomes]
rs34906981	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4500358	0.82[ASN][1000 genomes]
rs4596936	0.94[EUR][1000 genomes]
rs4916235	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4916400	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4916401	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4916402	0.82[ASN][1000 genomes]
rs4916403	0.82[ASN][1000 genomes]
rs4916404	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4916411	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6425454	0.82[ASN][1000 genomes]
rs6425455	0.82[ASN][1000 genomes]
rs6425456	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6425468	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425484	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6425518	0.87[EUR][1000 genomes]
rs6657315	0.82[ASN][1000 genomes]
rs6660011	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6665335	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6679341	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6683945	0.82[ASN][1000 genomes]
rs6685974	0.82[ASN][1000 genomes]
rs6686260	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6689231	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6690848	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6702944	0.82[ASN][1000 genomes]
rs71523161	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs742509	0.82[ASN][1000 genomes]
rs742510	0.82[ASN][1000 genomes]
rs7514627	0.82[ASN][1000 genomes]
rs7517331	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7526653	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7554700	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7554935	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs926545	0.82[ASN][1000 genomes]
rs926546	0.81[ASN][1000 genomes]
rs965051	0.82[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	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv831893	chr1:171802450-171985000	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171862200-171882600	Weak transcription	Aorta	Aorta
2	chr1:171868600-171880800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:171868800-171884000	Weak transcription	Fetal Lung	lung
4	chr1:171868800-171885000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:171872200-171883000	Weak transcription	Lung	lung
6	chr1:171878000-171881000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:171878000-171881000	Enhancers	HSMMtube	muscle
8	chr1:171878600-171882600	Enhancers	Brain Hippocampus Middle	brain
9	chr1:171879200-171881000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:171879400-171881200	Enhancers	NHEK	skin
11	chr1:171879600-171881000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:171879600-171881200	Enhancers	H9 Cell Line	embryonic stem cell
13	chr1:171879800-171880800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:171879800-171881000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr1:171879800-171881000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:171879800-171881600	Weak transcription	Brain Anterior Caudate	brain
17	chr1:171879800-171881800	Weak transcription	Brain Angular Gyrus	brain
18	chr1:171879800-171881800	Weak transcription	Fetal Brain Female	brain
19	chr1:171879800-171908000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:171880000-171881200	Enhancers	Psoas Muscle	Psoas
21	chr1:171880000-171882600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:171880000-171883800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:171880200-171881000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:171880200-171883800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:171880400-171880800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:171880400-171881800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:171880400-171882000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:171880400-171882000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:171880400-171882600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:171880400-171885600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:171880600-171881200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:171880600-171881400	Enhancers	Brain Substantia Nigra	brain
33	chr1:171880600-171881400	Enhancers	A549	lung
34	chr1:171880600-171881800	Weak transcription	HMEC	breast

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