Variant report

Variant	rs4653637
Chromosome Location	chr1:225624016-225624017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225620877..225622430-chr1:225623029..225626008,2	MCF-7	breast:
2	chr1:225622912..225625373-chr1:225627694..225629996,4	K562	blood:
3	chr1:225621659..225624533-chr1:225625428..225627724,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10753406	0.84[ASN][1000 genomes]
rs10799311	0.86[ASN][1000 genomes]
rs10799316	0.94[CHB][hapmap];0.83[CHD][hapmap];0.80[JPT][hapmap]
rs10799319	0.80[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs10915828	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10915830	0.93[ASN][1000 genomes]
rs10915833	0.85[ASN][1000 genomes]
rs10915847	0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs11584675	0.85[ASN][1000 genomes]
rs1222440	0.93[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap]
rs2066233	0.83[ASW][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs2185529	0.81[EUR][1000 genomes]
rs2639703	0.94[CHB][hapmap];0.81[CHD][hapmap]
rs3820226	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs4653639	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653643	0.87[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs487591	0.80[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs498350	0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs554744	0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs554992	0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs576861	0.94[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs6426076	0.86[ASN][1000 genomes]
rs6668770	0.81[ASN][1000 genomes]
rs6696038	0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs6697783	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6702452	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6702538	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6751	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.93[YRI][hapmap]
rs712062	0.94[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs7515907	0.86[ASN][1000 genomes]
rs7515939	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7541598	0.86[ASN][1000 genomes]
rs7549456	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7555553	0.86[ASN][1000 genomes]
rs947034	0.93[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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4653637	PYCR2	cis	cerebellum	SCAN
rs4653637	ENAH	cis	normal skin	skin_eQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225617400-225626600	Weak transcription	Dnd41	blood
2	chr1:225618400-225624600	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:225619600-225629000	Weak transcription	Spleen	Spleen
4	chr1:225621200-225625000	Enhancers	Thymus	Thymus
5	chr1:225621200-225626000	Enhancers	Primary B cells from peripheral blood	blood
6	chr1:225621400-225624600	Enhancers	Fetal Thymus	thymus
7	chr1:225622400-225626000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:225623000-225624800	Enhancers	K562	blood
9	chr1:225623000-225625400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:225623400-225624400	Enhancers	GM12878-XiMat	blood
11	chr1:225623800-225624200	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr1:225623800-225624600	Enhancers	Fetal Intestine Small	intestine
13	chr1:225623800-225624800	Enhancers	Fetal Intestine Large	intestine
14	chr1:225623800-225625800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:225624000-225624200	Bivalent Enhancer	HepG2	liver

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