Variant report

Variant	rs4670955
Chromosome Location	chr2:39963122-39963123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39962607..39965298-chr2:39967236..39969743,2	K562	blood:
2	chr2:39962720..39965298-chr2:39968180..39969743,3	K562	blood:
3	chr2:39961424..39963272-chr2:40004019..40005990,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10164984	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10169390	0.87[EUR][1000 genomes]
rs10174709	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10206408	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10207589	0.83[TSI][hapmap]
rs1035138	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1035139	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11124691	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11124692	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11124693	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs12470473	0.80[CEU][hapmap];0.93[CHD][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs12617624	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12620957	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12623462	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12623545	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12624217	0.92[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12712653	0.87[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs12712656	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13026313	0.80[CEU][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs13400213	0.85[EUR][1000 genomes]
rs13401182	0.81[AMR][1000 genomes]
rs13425906	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428837	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1548877	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17478972	0.92[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1861243	0.80[EUR][1000 genomes]
rs1986876	0.88[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2041735	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2058620	0.80[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2110656	0.93[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.85[ASN][1000 genomes]
rs2160198	0.88[CHB][hapmap]
rs2192685	0.96[CEU][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2373688	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2373689	0.80[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.87[ASN][1000 genomes]
rs2540226	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2540227	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2716704	0.82[ASN][1000 genomes]
rs2716727	0.86[ASN][1000 genomes]
rs2716729	0.80[ASN][1000 genomes]
rs2716730	0.93[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35761077	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3732121	0.86[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs3732122	0.80[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs4670956	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs4670957	0.81[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4670958	1.00[ASW][hapmap];0.81[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4670959	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59756273	0.87[ASN][1000 genomes]
rs6544242	0.80[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs6719179	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6731026	0.86[ASN][1000 genomes]
rs6731450	0.93[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs6747842	0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs6750252	0.92[ASN][1000 genomes]
rs6758453	0.87[CHB][hapmap];0.90[CHD][hapmap];0.85[ASN][1000 genomes]
rs727376	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7560642	0.84[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7565954	0.91[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7581406	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7590912	0.83[TSI][hapmap]
rs7591296	0.82[ASN][1000 genomes]
rs7591347	0.82[ASN][1000 genomes]
rs8265	0.92[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs917960	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs917962	0.80[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs917963	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9309042	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs962262	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs997976	0.80[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4670955	CYP1B1	cis	parietal	SCAN
rs4670955	THUMPD2	cis	cerebellum	SCAN
rs4670955	CCDC75	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39944400-39976600	Weak transcription	Fetal Brain Male	brain
2	chr2:39951000-39963600	Weak transcription	Pancreas	Pancrea
3	chr2:39951000-39964800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:39951200-39964800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:39951400-39963800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:39952000-39964800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:39956200-39966400	Weak transcription	Small Intestine	intestine
8	chr2:39956600-39963400	Weak transcription	Ovary	ovary
9	chr2:39956800-39964600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:39957400-39971200	Strong transcription	Primary T cells from cord blood	blood
11	chr2:39957600-39963200	Strong transcription	Fetal Lung	lung
12	chr2:39957600-39964200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:39958400-39963800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:39958800-39964400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr2:39958800-39964600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:39959000-39971200	Strong transcription	Fetal Thymus	thymus
17	chr2:39959400-39966400	Strong transcription	Fetal Intestine Large	intestine
18	chr2:39959400-39967400	Strong transcription	A549	lung
19	chr2:39959400-39971000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr2:39959400-39974200	Strong transcription	Primary B cells from cord blood	blood
21	chr2:39959600-39963800	Weak transcription	Esophagus	oesophagus
22	chr2:39959600-39967200	Strong transcription	HepG2	liver
23	chr2:39959800-39967000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr2:39960000-39963200	Weak transcription	Brain Germinal Matrix	brain
25	chr2:39960000-39964800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:39960000-39964800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:39960000-39969000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:39960000-39971000	Strong transcription	K562	blood
29	chr2:39960000-39971200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr2:39960000-39971400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:39960000-39971800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr2:39960200-39963800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:39960200-39963800	Weak transcription	Brain Anterior Caudate	brain
34	chr2:39960200-39965000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:39960200-39971000	Strong transcription	Fetal Muscle Leg	muscle
36	chr2:39960200-39973800	Strong transcription	Primary hematopoietic stem cells	blood
37	chr2:39960200-39987200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:39960400-39965000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:39960400-39970200	Strong transcription	GM12878-XiMat	blood
40	chr2:39960400-39973600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:39960400-39983000	Weak transcription	Stomach Mucosa	stomach
42	chr2:39960600-39963800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr2:39960600-39963800	Weak transcription	Psoas Muscle	Psoas
44	chr2:39960600-39964600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:39960800-39964600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:39960800-39964800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:39961000-39966200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr2:39961200-39964000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:39961200-39974600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:39961400-39964200	Strong transcription	HUES64 Cell Line	embryonic stem cell

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