Variant report

Variant	rs2654949
Chromosome Location	chr4:148583291-148583292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10015717	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1005871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10305871	1.00[CEU][hapmap]
rs10519911	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11099668	0.87[ASN][1000 genomes]
rs12507247	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12510847	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12510915	0.84[ASN][1000 genomes]
rs13108782	0.94[ASN][1000 genomes]
rs17023732	0.82[CHB][hapmap]
rs17675572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2036498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2036500	0.88[ASN][1000 genomes]
rs2036501	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2357926	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2358097	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2654937	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2654938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2654940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[ASN][1000 genomes]
rs2654941	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2654948	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2718447	0.92[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2718448	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2718449	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2718452	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2718453	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2718454	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2718455	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2718457	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2718458	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2884383	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4379049	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs4835441	0.91[ASN][1000 genomes]
rs4835445	0.93[ASN][1000 genomes]
rs57690385	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60862021	0.83[ASN][1000 genomes]
rs6535552	0.94[ASN][1000 genomes]
rs6535553	0.93[ASN][1000 genomes]
rs6535554	0.93[ASN][1000 genomes]
rs6535555	0.89[ASN][1000 genomes]
rs6810521	0.89[ASN][1000 genomes]
rs6828566	0.88[ASN][1000 genomes]
rs6841745	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6845224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6845592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[ASN][1000 genomes]
rs6846220	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7655893	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7660361	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7664244	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7666065	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7672671	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7675850	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7678612	0.88[ASN][1000 genomes]
rs7687368	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7690974	0.92[ASN][1000 genomes]
rs884761	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs905606	0.81[JPT][hapmap]
rs905607	0.87[ASN][1000 genomes]
rs924783	0.92[ASN][1000 genomes]
rs9998065	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830110	chr4:148432125-148595119	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv428776	chr4:148432125-148595119	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148548400-148599800	Weak transcription	Gastric	stomach
2	chr4:148548600-148604400	Weak transcription	Esophagus	oesophagus
3	chr4:148549000-148599800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:148551400-148603600	Weak transcription	Hela-S3	cervix
5	chr4:148554600-148604600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:148556000-148603800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:148556400-148599600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:148556600-148595200	Weak transcription	NHLF	lung
9	chr4:148557400-148603800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:148557600-148594000	Weak transcription	NHEK	skin
11	chr4:148557800-148603800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:148558200-148603800	Weak transcription	A549	lung
13	chr4:148558400-148603800	Weak transcription	HUVEC	blood vessel
14	chr4:148559400-148599200	Weak transcription	HMEC	breast
15	chr4:148561200-148596200	Weak transcription	NHDF-Ad	bronchial
16	chr4:148562800-148585000	Weak transcription	Fetal Brain Male	brain
17	chr4:148562800-148603800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:148562800-148604200	Weak transcription	Right Ventricle	heart
19	chr4:148563600-148604400	Weak transcription	Pancreas	Pancrea
20	chr4:148563800-148599800	Weak transcription	Spleen	Spleen
21	chr4:148565000-148602200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr4:148568400-148603800	Weak transcription	Fetal Kidney	kidney
23	chr4:148568800-148584000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:148568800-148600400	Weak transcription	Psoas Muscle	Psoas
25	chr4:148569400-148604000	Weak transcription	Brain Hippocampus Middle	brain
26	chr4:148570200-148599400	Weak transcription	K562	blood
27	chr4:148570400-148595800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:148570400-148604200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:148571600-148603800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:148572800-148585600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:148573800-148587200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:148574000-148584000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr4:148574000-148589800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr4:148574200-148584000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr4:148574200-148584200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:148574600-148596800	Strong transcription	Primary T cells from cord blood	blood
37	chr4:148574800-148583800	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr4:148574800-148585400	Strong transcription	Liver	Liver
39	chr4:148574800-148586800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr4:148575600-148599800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:148575600-148604000	Weak transcription	Brain Substantia Nigra	brain
42	chr4:148575800-148599600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:148576400-148585600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:148576400-148603800	Weak transcription	Small Intestine	intestine
45	chr4:148577000-148604400	Weak transcription	Aorta	Aorta
46	chr4:148577200-148589400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr4:148577200-148595800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr4:148577200-148604000	Weak transcription	Colonic Mucosa	Colon
49	chr4:148577400-148583800	Strong transcription	Ovary	ovary
50	chr4:148577400-148604600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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