Variant report

Variant	rs2654940
Chromosome Location	chr4:148544281-148544282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:148542240..148544563-chr4:148545277..148546786,2	K562	blood:
2	chr4:148544238..148546653-chr4:148547718..148550909,3	K562	blood:

Variant related genes	Relation type
ENSG00000164168	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10015717	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[ASN][1000 genomes]
rs1005871	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10519911	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11099668	0.82[ASN][1000 genomes]
rs12507247	0.91[ASN][1000 genomes]
rs12510847	0.83[ASN][1000 genomes]
rs12510915	0.80[ASN][1000 genomes]
rs13108782	0.90[ASN][1000 genomes]
rs17023732	0.82[CHB][hapmap]
rs17675572	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2036498	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[ASN][1000 genomes]
rs2036500	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2036501	0.93[ASN][1000 genomes]
rs2357926	0.88[ASW][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[ASN][1000 genomes]
rs2358097	0.82[CHB][hapmap]
rs2654937	0.83[ASW][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.99[ASN][1000 genomes]
rs2654938	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2654941	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[ASN][1000 genomes]
rs2654948	0.93[ASN][1000 genomes]
rs2654949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[ASN][1000 genomes]
rs2718447	0.88[ASW][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.99[ASN][1000 genomes]
rs2718448	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.97[ASN][1000 genomes]
rs2718449	0.94[ASN][1000 genomes]
rs2718452	0.90[ASN][1000 genomes]
rs2718453	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[ASN][1000 genomes]
rs2718454	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[ASN][1000 genomes]
rs2718455	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[ASN][1000 genomes]
rs2718457	0.90[ASN][1000 genomes]
rs2718458	0.95[ASN][1000 genomes]
rs2884383	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[ASN][1000 genomes]
rs4379049	0.82[CHB][hapmap]
rs4835439	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4835440	0.98[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4835441	0.87[ASN][1000 genomes]
rs4835445	0.89[ASN][1000 genomes]
rs57690385	0.93[ASN][1000 genomes]
rs60862021	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6535552	0.90[ASN][1000 genomes]
rs6535553	0.89[ASN][1000 genomes]
rs6535554	0.89[ASN][1000 genomes]
rs6535555	0.84[ASN][1000 genomes]
rs6810521	0.84[ASN][1000 genomes]
rs6828566	0.83[ASN][1000 genomes]
rs6841745	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[ASN][1000 genomes]
rs6845224	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6845592	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6846220	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7655893	0.91[ASN][1000 genomes]
rs7660361	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[ASN][1000 genomes]
rs7664244	0.85[ASN][1000 genomes]
rs7666065	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[ASN][1000 genomes]
rs7672671	0.87[ASN][1000 genomes]
rs7675850	0.91[ASN][1000 genomes]
rs7678612	0.84[ASN][1000 genomes]
rs7687368	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[ASN][1000 genomes]
rs7690974	0.88[ASN][1000 genomes]
rs884761	0.88[ASW][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[ASN][1000 genomes]
rs905607	0.82[ASN][1000 genomes]
rs924783	0.88[ASN][1000 genomes]
rs9998065	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1019205	chr4:148524852-148576265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148539400-148547000	Weak transcription	Lung	lung
2	chr4:148539400-148547200	Weak transcription	Esophagus	oesophagus
3	chr4:148539400-148548200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:148539400-148576800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:148539600-148546800	Weak transcription	Colonic Mucosa	Colon
6	chr4:148539600-148547000	Weak transcription	Aorta	Aorta
7	chr4:148539600-148547800	Weak transcription	HSMMtube	muscle
8	chr4:148539600-148554200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:148539800-148544600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:148539800-148545000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:148539800-148546600	Weak transcription	NHLF	lung
12	chr4:148539800-148547600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:148539800-148550000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:148539800-148557200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:148540200-148547000	Weak transcription	Pancreas	Pancrea
16	chr4:148540800-148561000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:148541000-148545000	Strong transcription	Fetal Muscle Leg	muscle
18	chr4:148541000-148549600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr4:148541400-148546000	Weak transcription	Brain Substantia Nigra	brain
20	chr4:148541400-148546400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:148541400-148554800	Weak transcription	A549	lung
22	chr4:148541400-148563400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:148541600-148546400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:148542000-148544800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:148542000-148545000	Weak transcription	HMEC	breast
26	chr4:148542200-148545000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:148542200-148545600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr4:148542200-148546000	Weak transcription	Colon Smooth Muscle	Colon
29	chr4:148542200-148547000	Weak transcription	Thymus	Thymus
30	chr4:148542200-148564200	Strong transcription	Fetal Thymus	thymus
31	chr4:148542400-148544600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:148542400-148545000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:148542400-148545000	Weak transcription	HepG2	liver
34	chr4:148542400-148545800	Weak transcription	NHEK	skin
35	chr4:148542400-148546000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:148542400-148546000	Weak transcription	Hela-S3	cervix
37	chr4:148542400-148547000	Weak transcription	Gastric	stomach
38	chr4:148542400-148547600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:148542400-148547600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr4:148542400-148548000	Weak transcription	Psoas Muscle	Psoas
41	chr4:148542400-148560400	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr4:148542400-148562200	Weak transcription	Fetal Brain Male	brain
43	chr4:148542400-148575000	Weak transcription	Small Intestine	intestine
44	chr4:148542400-148576600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr4:148542600-148544600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:148542600-148545000	Weak transcription	NH-A	brain
47	chr4:148542600-148545800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:148542600-148546800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:148542600-148546800	Weak transcription	Ovary	ovary
50	chr4:148542600-148547600	Weak transcription	Brain Cingulate Gyrus	brain

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