Variant report

Variant	rs1545840
Chromosome Location	chr6:149212595-149212596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10499259	0.90[CHB][hapmap];0.82[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11756841	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11757486	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11758175	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11758187	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11758230	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11759833	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1340498	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1340499	0.89[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1351698	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1351699	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1545841	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545842	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17079451	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17079511	0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1817508	0.90[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34443186	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35526080	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35748463	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35946167	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56904209	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426102	0.82[ASN][1000 genomes]
rs62426104	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62426110	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv464074	chr6:149211090-149242095	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv604844	chr6:149211090-149242095	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149193200-149218800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:149199400-149215600	Weak transcription	Spleen	Spleen
3	chr6:149203400-149213400	Weak transcription	Dnd41	blood
4	chr6:149206000-149212600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:149206200-149212600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:149207400-149214800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:149207800-149219400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:149207800-149221400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:149207800-149237400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:149208000-149217200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:149208000-149229800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:149208600-149213200	Weak transcription	NHLF	lung
13	chr6:149209000-149212600	Enhancers	Ovary	ovary
14	chr6:149209000-149213200	Weak transcription	NHEK	skin
15	chr6:149209000-149247600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:149209600-149213200	Enhancers	Fetal Heart	heart
17	chr6:149209600-149214800	Weak transcription	Fetal Stomach	stomach
18	chr6:149209800-149230800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:149210000-149218000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr6:149210000-149220800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:149210200-149212600	Enhancers	Aorta	Aorta
22	chr6:149210200-149212600	Enhancers	Fetal Lung	lung
23	chr6:149210200-149212600	Enhancers	Right Atrium	heart
24	chr6:149210200-149212600	Enhancers	Osteobl	bone
25	chr6:149210200-149212800	Enhancers	Stomach Mucosa	stomach
26	chr6:149210200-149230200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr6:149210200-149240200	Weak transcription	Primary B cells from cord blood	blood
28	chr6:149210400-149214800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:149210400-149226200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:149210400-149235000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr6:149210800-149226000	Weak transcription	Esophagus	oesophagus
32	chr6:149211000-149215000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:149211000-149216600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:149211000-149221000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:149211000-149221400	Weak transcription	Lung	lung
36	chr6:149211200-149212600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:149211200-149213200	Enhancers	Liver	Liver
38	chr6:149211400-149212600	Enhancers	Fetal Brain Male	brain
39	chr6:149211600-149212600	Bivalent Enhancer	HepG2	liver
40	chr6:149211600-149213600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:149211600-149214400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:149211600-149226400	Weak transcription	Left Ventricle	heart
43	chr6:149211600-149255400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr6:149212200-149212600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr6:149212200-149212800	Enhancers	Gastric	stomach
46	chr6:149212200-149213000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:149212200-149230200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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