Variant report

Variant	rs62534459
Chromosome Location	chr9:7059058-7059059
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10429452	0.89[EUR][1000 genomes]
rs10975977	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10975979	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10975982	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10975983	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10976002	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10976003	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10976004	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10976011	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10976016	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10976034	0.87[EUR][1000 genomes]
rs12235561	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12236257	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1323402	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1407859	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1575451	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1578326	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16925141	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16925300	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2297963	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2890734	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2890735	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56063552	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60485419	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62533861	0.89[EUR][1000 genomes]
rs62534416	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6477148	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6477151	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7021973	0.89[EUR][1000 genomes]
rs7024887	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7026804	0.87[EUR][1000 genomes]
rs7031605	0.89[EUR][1000 genomes]
rs7032864	0.89[EUR][1000 genomes]
rs7036253	0.89[EUR][1000 genomes]
rs7038205	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72703338	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72703343	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73401806	0.91[ASN][1000 genomes]
rs7848775	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8181057	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181075	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs818881	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
3	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv892185	chr9:6929053-7070962	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv870178	chr9:6941584-7060029	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv892186	chr9:6942605-7075305	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1024763	chr9:7022554-7061314	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv466117	chr9:7030268-7084558	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv613258	chr9:7030268-7084558	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv613259	chr9:7032776-7541338	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv1015874	chr9:7048807-7434890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	nsv539971	chr9:7048807-7434890	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7009000-7076600	Weak transcription	HSMM	muscle
2	chr9:7009200-7077600	Weak transcription	Osteobl	bone
3	chr9:7009800-7076600	Weak transcription	HSMMtube	muscle
4	chr9:7012200-7111200	Weak transcription	Colonic Mucosa	Colon
5	chr9:7012800-7076800	Weak transcription	Pancreas	Pancrea
6	chr9:7017800-7075000	Weak transcription	HepG2	liver
7	chr9:7018800-7064400	Weak transcription	Psoas Muscle	Psoas
8	chr9:7028400-7076800	Weak transcription	Placenta	Placenta
9	chr9:7028800-7076400	Weak transcription	Aorta	Aorta
10	chr9:7028800-7077000	Weak transcription	Esophagus	oesophagus
11	chr9:7028800-7086400	Weak transcription	Right Ventricle	heart
12	chr9:7029000-7061400	Weak transcription	Fetal Intestine Small	intestine
13	chr9:7029000-7076400	Weak transcription	Ovary	ovary
14	chr9:7029000-7076600	Weak transcription	Lung	lung
15	chr9:7029000-7077400	Weak transcription	Gastric	stomach
16	chr9:7029000-7081200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:7034000-7103600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr9:7043000-7069400	Weak transcription	NHDF-Ad	bronchial
19	chr9:7043400-7103600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:7045000-7059200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:7045400-7077000	Weak transcription	Fetal Muscle Leg	muscle
22	chr9:7045400-7077000	Weak transcription	HMEC	breast
23	chr9:7046400-7077000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr9:7047600-7061400	Weak transcription	Spleen	Spleen
25	chr9:7049200-7075600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:7049400-7076000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr9:7050000-7076800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr9:7050000-7082200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr9:7050200-7076600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr9:7050400-7061400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr9:7050400-7076400	Weak transcription	Dnd41	blood
32	chr9:7051000-7068600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:7051600-7103200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr9:7051800-7076200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr9:7052000-7064000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr9:7052000-7074800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:7052000-7075800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr9:7052000-7076400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr9:7052600-7086400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:7053000-7060200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr9:7053000-7076200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr9:7053000-7076200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr9:7053000-7086600	Weak transcription	Fetal Intestine Large	intestine
44	chr9:7053200-7076600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:7053200-7077000	Weak transcription	Brain Angular Gyrus	brain
46	chr9:7053200-7084400	Weak transcription	Brain Hippocampus Middle	brain
47	chr9:7053200-7099200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr9:7054400-7077400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr9:7054600-7064200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr9:7055200-7069000	Weak transcription	Duodenum Mucosa	Duodenum

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