Variant report

Variant	rs8265
Chromosome Location	chr2:39963667-39963668
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	chr2:39956511..39959313-chr2:39963423..39966222,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10164984	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10169390	0.83[ASN][1000 genomes]
rs10174709	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10207589	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10211306	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1035138	0.81[EUR][1000 genomes]
rs1035139	0.81[EUR][1000 genomes]
rs11124692	0.86[ASN][1000 genomes]
rs11124693	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11684302	0.85[CEU][hapmap]
rs12470473	0.89[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12617624	0.88[EUR][1000 genomes]
rs12624217	0.85[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs12712656	0.84[CEU][hapmap];0.90[CHB][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13026313	0.89[CEU][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs13400213	0.87[ASN][1000 genomes]
rs13425906	0.87[EUR][1000 genomes]
rs13428837	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1548877	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17478972	0.85[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1861243	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1861258	0.85[CEU][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1986876	0.82[CEU][hapmap]
rs2041735	0.90[EUR][1000 genomes]
rs2058620	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2110656	0.80[ASW][hapmap];0.85[CEU][hapmap];0.83[MEX][hapmap];0.85[EUR][1000 genomes]
rs2160199	0.85[ASW][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2192685	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2192686	0.86[AFR][1000 genomes]
rs2241115	1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs2373689	0.89[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2540226	0.92[EUR][1000 genomes]
rs2540227	0.92[EUR][1000 genomes]
rs2540228	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2540229	0.82[AMR][1000 genomes]
rs2716681	0.87[AFR][1000 genomes]
rs2716729	0.86[EUR][1000 genomes]
rs2716730	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs3732121	0.86[EUR][1000 genomes]
rs3732122	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs3815510	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4670955	0.87[EUR][1000 genomes]
rs4670956	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs4670959	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs56721088	0.88[EUR][1000 genomes]
rs59756273	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6544242	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6719179	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs6722610	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6731026	0.84[EUR][1000 genomes]
rs6731450	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs727376	0.81[EUR][1000 genomes]
rs7560642	0.92[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs7590912	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7591296	0.83[EUR][1000 genomes]
rs7591347	0.88[EUR][1000 genomes]
rs917960	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs917961	0.85[ASW][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs917962	0.89[CEU][hapmap];0.83[MEX][hapmap];0.90[EUR][1000 genomes]
rs917963	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs9309042	0.81[EUR][1000 genomes]
rs997976	0.89[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][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
rs8265	TMEM178	cis	cerebellum	SCAN
rs8265	THUMPD2	cis	cerebellum	SCAN
rs8265	CYP1B1	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	chr2:39951000-39964800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:39951200-39964800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:39951400-39963800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:39952000-39964800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:39956200-39966400	Weak transcription	Small Intestine	intestine
7	chr2:39956800-39964600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:39957400-39971200	Strong transcription	Primary T cells from cord blood	blood
9	chr2:39957600-39964200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:39958400-39963800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr2:39958800-39964400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr2:39958800-39964600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:39959000-39971200	Strong transcription	Fetal Thymus	thymus
14	chr2:39959400-39966400	Strong transcription	Fetal Intestine Large	intestine
15	chr2:39959400-39967400	Strong transcription	A549	lung
16	chr2:39959400-39971000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:39959400-39974200	Strong transcription	Primary B cells from cord blood	blood
18	chr2:39959600-39963800	Weak transcription	Esophagus	oesophagus
19	chr2:39959600-39967200	Strong transcription	HepG2	liver
20	chr2:39959800-39967000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:39960000-39964800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:39960000-39964800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:39960000-39969000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:39960000-39971000	Strong transcription	K562	blood
25	chr2:39960000-39971200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr2:39960000-39971400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:39960000-39971800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr2:39960200-39963800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:39960200-39963800	Weak transcription	Brain Anterior Caudate	brain
30	chr2:39960200-39965000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:39960200-39971000	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:39960200-39973800	Strong transcription	Primary hematopoietic stem cells	blood
33	chr2:39960200-39987200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:39960400-39965000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:39960400-39970200	Strong transcription	GM12878-XiMat	blood
36	chr2:39960400-39973600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:39960400-39983000	Weak transcription	Stomach Mucosa	stomach
38	chr2:39960600-39963800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:39960600-39963800	Weak transcription	Psoas Muscle	Psoas
40	chr2:39960600-39964600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:39960800-39964600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:39960800-39964800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:39961000-39966200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr2:39961200-39964000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:39961200-39974600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:39961400-39964200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:39961400-39969800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:39961400-39984200	Weak transcription	Colonic Mucosa	Colon
49	chr2:39961600-39968800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:39961600-39971200	Strong transcription	Dnd41	blood

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