Variant report

Variant	rs1949652
Chromosome Location	chr2:213110424-213110425
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:213108853..213110992-chr2:213114605..213117467,2	MCF-7	breast:
2	chr2:213110335..213112278-chr2:213114371..213115906,2	MCF-7	breast:

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10048673	0.85[CEU][hapmap];0.80[CHB][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap]
rs10048750	0.84[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10048796	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs10048819	0.85[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10166172	0.85[CEU][hapmap];0.80[CHB][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap]
rs10168128	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10168303	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10172782	0.92[CHB][hapmap]
rs10196229	0.84[CEU][hapmap]
rs10201835	0.88[ASN][1000 genomes]
rs10206443	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs10207020	0.90[ASN][1000 genomes]
rs10932428	0.87[CHB][hapmap]
rs11676942	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11677095	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11677623	0.88[CEU][hapmap];0.80[CHB][hapmap]
rs11682936	0.93[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11694300	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11887771	0.85[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs11896691	0.93[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs11902860	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12185587	0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12622947	0.80[CHB][hapmap]
rs13391312	0.80[CHB][hapmap]
rs13407289	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs13408933	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13415721	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13426969	0.88[ASN][1000 genomes]
rs13427258	0.84[CHB][hapmap]
rs13428714	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13429136	0.85[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13432680	0.80[CHB][hapmap]
rs1357136	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1357137	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1357138	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1402762	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1402764	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1521634	0.80[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1521638	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1521639	0.93[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1521641	0.87[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1521642	0.88[ASN][1000 genomes]
rs1521643	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1521644	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1521645	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1521649	0.85[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs1521662	0.88[CHB][hapmap];0.91[CHD][hapmap]
rs1546718	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1546719	0.84[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1851285	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1851286	0.89[ASN][1000 genomes]
rs1915747	0.91[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1915748	0.81[CHB][hapmap]
rs1948875	0.81[CHB][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1949651	0.88[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1949653	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1949654	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1976839	0.84[ASN][1000 genomes]
rs2030474	0.95[ASN][1000 genomes]
rs2049180	0.84[CEU][hapmap];0.80[CHB][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs2090862	0.80[CHB][hapmap]
rs2103001	0.80[CHB][hapmap]
rs2139971	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4233985	0.85[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4350692	0.85[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs4375810	0.85[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4580336	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs4638732	0.85[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs4672641	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4672643	0.85[CEU][hapmap];0.88[CHB][hapmap];0.87[EUR][1000 genomes]
rs4673654	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4673657	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs6724508	0.87[ASN][1000 genomes]
rs6727447	1.00[CHB][hapmap]
rs6727639	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6742273	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6745160	0.88[CEU][hapmap];0.84[CHD][hapmap];0.86[EUR][1000 genomes]
rs6745249	0.80[CEU][hapmap];0.84[CHD][hapmap]
rs6755951	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7560301	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7561603	0.88[CEU][hapmap];0.81[CHB][hapmap];0.87[EUR][1000 genomes]
rs7570768	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs7581138	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7592673	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9288446	0.80[CHB][hapmap]
rs9288447	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs9288449	0.87[CHB][hapmap]
rs939224	0.85[CEU][hapmap];0.93[CHB][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap]
rs939226	0.82[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs9653257	0.80[CHB][hapmap]
rs9973520	0.80[CHB][hapmap]
rs9973523	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011572	chr2:212840066-213152279	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv875805	chr2:212891401-213164837	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv875806	chr2:212997024-213211067	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1001718	chr2:213047033-213155985	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1004823	chr2:213052804-213181263	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv536138	chr2:213052804-213181263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1006051	chr2:213052804-213273642	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv584346	chr2:213067749-213258622	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv998615	chr2:213081893-213202228	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
10	nsv536139	chr2:213081893-213202228	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
11	nsv1007853	chr2:213087904-213134413	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1949652	FN1	cis	cerebellum	SCAN
rs1949652	VWC2L	cis	cerebellum	SCAN
rs1949652	ERBB4	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:213107800-213110600	Weak transcription	Fetal Heart	heart
2	chr2:213107800-213134000	Weak transcription	Aorta	Aorta
3	chr2:213110200-213110600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:213110400-213111400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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