Variant report

Variant	rs612262
Chromosome Location	chr6:35891608-35891609
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35891486..35893902-chr6:35896249..35898461,2	K562	blood:
2	chr6:35888847..35890514-chr6:35891095..35893744,2	MCF-7	breast:
3	chr6:35891486..35894129-chr6:35896890..35898461,2	K562	blood:
4	chr6:35884518..35891365-chr6:35891420..35897424,10	K562	blood:
5	chr6:35889868..35892121-chr6:35927053..35928934,3	K562	blood:

Variant related genes	Relation type
ENSG00000096063	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1049649	0.85[CEU][hapmap]
rs10947572	0.82[CEU][hapmap]
rs1160828	0.85[CEU][hapmap]
rs11755072	0.85[CEU][hapmap]
rs1326752	0.85[CEU][hapmap]
rs17653835	0.85[CEU][hapmap]
rs17705020	0.85[CEU][hapmap]
rs2038961	0.90[EUR][1000 genomes]
rs2051647	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs2301510	0.85[CEU][hapmap]
rs2395640	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs2766522	0.88[EUR][1000 genomes]
rs2766527	0.88[EUR][1000 genomes]
rs2766528	0.90[EUR][1000 genomes]
rs2817027	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs2859420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3213580	0.86[CEU][hapmap]
rs3761981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3891863	0.85[CEU][hapmap]
rs4340986	0.85[CEU][hapmap]
rs4713929	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs595591	0.80[GIH][hapmap]
rs608267	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs619264	0.80[EUR][1000 genomes]
rs638600	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs639421	0.85[CEU][hapmap]
rs6457858	0.82[CEU][hapmap]
rs6457862	0.85[CEU][hapmap]
rs651158	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs661337	0.80[EUR][1000 genomes]
rs662713	0.82[CEU][hapmap]
rs668438	0.80[GIH][hapmap]
rs677937	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs6908433	0.85[CEU][hapmap]
rs6909895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6911849	0.85[CEU][hapmap]
rs6916941	0.91[CEU][hapmap]
rs6920616	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6920862	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6923015	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs6929493	0.85[CEU][hapmap]
rs6931888	0.82[CEU][hapmap]
rs6932973	0.85[CEU][hapmap]
rs6933241	0.91[EUR][1000 genomes]
rs7740886	0.82[CEU][hapmap]
rs7752545	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs7752551	0.85[CEU][hapmap]
rs7755022	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7755600	0.85[CEU][hapmap]
rs879493	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs879667	0.86[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs9296168	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs9462128	0.85[CEU][hapmap]
rs9462132	0.85[CEU][hapmap]
rs9462134	0.85[CEU][hapmap]
rs9462135	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs9462141	0.85[CEU][hapmap]
rs9462143	0.85[CEU][hapmap]
rs9470120	0.85[CEU][hapmap]
rs9470121	0.85[CEU][hapmap]
rs9470126	0.85[CEU][hapmap]
rs9470131	0.85[CEU][hapmap]
rs9470134	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9470138	0.85[CEU][hapmap]
rs9470139	0.85[CEU][hapmap]
rs9470141	0.85[CEU][hapmap]
rs9470144	0.85[CEU][hapmap]
rs9470147	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs9470152	0.85[CEU][hapmap]
rs9470153	0.85[CEU][hapmap]
rs9470154	0.85[CEU][hapmap]
rs9470155	0.85[CEU][hapmap]
rs9470156	0.84[CEU][hapmap]
rs9470162	0.85[CEU][hapmap]
rs9470171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9470172	0.85[CEU][hapmap]

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	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3363467	chr6:35820920-36222197	Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs612262	BRPF3	cis	cerebellum	SCAN
rs612262	CDKN1A	cis	cerebellum	SCAN
rs612262	C6orf106	cis	cerebellum	SCAN
rs612262	SRPK1	cis	parietal	SCAN
rs612262	SRPK1	cis	cerebellum	SCAN
rs612262	LHFPL5	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35889200-35893800	Weak transcription	Lung	lung
2	chr6:35889200-35898600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:35889400-35893400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:35889400-35893600	Weak transcription	Esophagus	oesophagus
5	chr6:35889400-35893800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:35889400-35895600	Weak transcription	Placenta	Placenta
7	chr6:35889400-35898600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:35889800-35893600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:35889800-35893800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:35889800-35901600	Weak transcription	Psoas Muscle	Psoas
11	chr6:35890400-35893600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:35890400-35893600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:35890400-35930200	Weak transcription	Pancreas	Pancrea
14	chr6:35890600-35893800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:35890800-35892000	Enhancers	HepG2	liver
16	chr6:35890800-35894400	Weak transcription	K562	blood
17	chr6:35891000-35900400	Weak transcription	Fetal Intestine Small	intestine

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