Variant report

Variant	rs2602376
Chromosome Location	chr2:234582051-234582052
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10167119	0.81[GIH][hapmap]
rs10168416	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs10173355	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs10197460	0.81[GIH][hapmap]
rs10202865	0.90[CEU][hapmap]
rs11692664	0.81[EUR][1000 genomes]
rs13009407	0.84[CEU][hapmap]
rs17863787	0.85[CEU][hapmap];0.82[GIH][hapmap]
rs2070959	0.85[CEU][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs2602362	0.86[ASN][1000 genomes]
rs2602373	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2602374	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2741012	0.86[ASN][1000 genomes]
rs2741013	0.86[ASN][1000 genomes]
rs2741019	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2741021	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs2741022	0.86[ASN][1000 genomes]
rs2741023	0.86[ASN][1000 genomes]
rs2741027	0.86[ASN][1000 genomes]
rs2741029	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap]
rs2741030	1.00[CHB][hapmap];0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs2741034	0.86[ASN][1000 genomes]
rs2741036	1.00[CHB][hapmap];0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs2741038	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2741042	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2741044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28898569	1.00[YRI][hapmap]
rs28898572	1.00[YRI][hapmap]
rs28898588	1.00[YRI][hapmap]
rs28898597	1.00[YRI][hapmap]
rs28898607	1.00[YRI][hapmap]
rs28898610	1.00[YRI][hapmap]
rs28898618	1.00[YRI][hapmap]
rs28899169	1.00[YRI][hapmap]
rs28899170	0.90[CEU][hapmap]
rs28899184	1.00[YRI][hapmap]
rs28899185	1.00[YRI][hapmap]
rs28969677	1.00[YRI][hapmap]
rs28969714	1.00[YRI][hapmap]
rs4148324	0.81[CEU][hapmap]
rs4148325	0.81[CEU][hapmap]
rs6742078	0.81[CEU][hapmap]
rs6746419	1.00[YRI][hapmap]
rs7571915	0.83[EUR][1000 genomes]
rs7586110	0.81[GIH][hapmap]
rs887829	0.81[CEU][hapmap]
rs929596	0.84[CEU][hapmap]

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	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	esv3340677	chr2:234580879-234591324	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2602376	ITM2C	cis	cerebellum	SCAN
rs2602376	NPPC	cis	parietal	SCAN
rs2602376	EFHD1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234554600-234587800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:234559800-234592800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:234580400-234582200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr2:234580600-234582400	Active TSS	Liver	Liver
5	chr2:234580600-234582400	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links