Variant report

Variant	rs4742290
Chromosome Location	chr9:7039410-7039411
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10975987	1.00[CEU][hapmap]
rs12551096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12554351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12555355	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12555356	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12555619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16925158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16925172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16925187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16925196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16925262	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2381543	1.00[CEU][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4587383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4642706	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4742284	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs4742286	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742291	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742295	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs61567339	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401803	0.82[AFR][1000 genomes]
rs73401836	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401840	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73401842	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403535	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7850439	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854837	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs7859954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs995134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[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	nsv831501	chr9:6868099-7058526	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv949711	chr9:6994399-7045058	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7009000-7044800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr9:7009000-7046200	Weak transcription	Small Intestine	intestine
3	chr9:7009000-7055200	Weak transcription	K562	blood
4	chr9:7009000-7056400	Weak transcription	Brain Substantia Nigra	brain
5	chr9:7009000-7076600	Weak transcription	HSMM	muscle
6	chr9:7009200-7077600	Weak transcription	Osteobl	bone
7	chr9:7009400-7042000	Weak transcription	NHDF-Ad	bronchial
8	chr9:7009800-7076600	Weak transcription	HSMMtube	muscle
9	chr9:7011800-7048800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr9:7012200-7046800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr9:7012200-7052600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:7012200-7111200	Weak transcription	Colonic Mucosa	Colon
13	chr9:7012800-7048800	Weak transcription	Dnd41	blood
14	chr9:7012800-7076800	Weak transcription	Pancreas	Pancrea
15	chr9:7014600-7048000	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:7017800-7075000	Weak transcription	HepG2	liver
17	chr9:7018600-7044600	Weak transcription	GM12878-XiMat	blood
18	chr9:7018600-7049600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr9:7018800-7041600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:7018800-7047200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr9:7018800-7047800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:7018800-7064400	Weak transcription	Psoas Muscle	Psoas
23	chr9:7019600-7046800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr9:7020000-7052800	Weak transcription	NHLF	lung
25	chr9:7027800-7041800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:7028000-7046400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr9:7028000-7047000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr9:7028000-7048800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr9:7028400-7052800	Weak transcription	Brain Hippocampus Middle	brain
30	chr9:7028400-7076800	Weak transcription	Placenta	Placenta
31	chr9:7028600-7046400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:7028800-7046400	Weak transcription	Thymus	Thymus
33	chr9:7028800-7046600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr9:7028800-7046800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:7028800-7046800	Weak transcription	Liver	Liver
36	chr9:7028800-7047000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr9:7028800-7047800	Weak transcription	Fetal Intestine Large	intestine
38	chr9:7028800-7048000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr9:7028800-7076400	Weak transcription	Aorta	Aorta
40	chr9:7028800-7077000	Weak transcription	Esophagus	oesophagus
41	chr9:7028800-7086400	Weak transcription	Right Ventricle	heart
42	chr9:7029000-7041800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr9:7029000-7042000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr9:7029000-7045000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:7029000-7045600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr9:7029000-7046200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr9:7029000-7046400	Weak transcription	Adipose Nuclei	Adipose
48	chr9:7029000-7047800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr9:7029000-7052600	Weak transcription	Brain Anterior Caudate	brain
50	chr9:7029000-7061400	Weak transcription	Fetal Intestine Small	intestine

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