Variant report

Variant	rs1948875
Chromosome Location	chr2:213122718-213122719
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10048673	0.87[CHD][hapmap];0.89[TSI][hapmap]
rs10048750	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10048796	0.81[CHB][hapmap]
rs10048819	0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10166172	0.80[CHD][hapmap];0.89[TSI][hapmap]
rs10168128	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10168303	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10172782	0.92[CHB][hapmap]
rs10201835	0.91[ASN][1000 genomes]
rs10207020	0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10932428	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs11676942	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11677095	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11682936	0.87[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs11693640	0.83[CHD][hapmap]
rs11694300	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11887771	0.87[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11896691	0.87[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11902860	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12185587	0.92[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12622947	0.84[CHD][hapmap]
rs13391312	0.87[CHD][hapmap]
rs13408933	0.87[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13415721	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13426969	0.87[ASN][1000 genomes]
rs13428714	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13429136	0.87[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13432680	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs1357136	0.81[CHB][hapmap];0.86[ASN][1000 genomes]
rs1357137	0.86[ASN][1000 genomes]
rs1357138	0.87[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1402762	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1402764	0.87[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1402769	0.87[CHD][hapmap]
rs1521634	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs1521638	0.86[ASN][1000 genomes]
rs1521639	0.87[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1521641	0.81[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1521642	0.90[ASN][1000 genomes]
rs1521643	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1521644	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1521645	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1521649	0.83[CHD][hapmap];0.85[TSI][hapmap]
rs1521662	0.81[CHB][hapmap]
rs1546718	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs1546719	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs1851285	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1851286	0.91[ASN][1000 genomes]
rs1915747	0.93[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1949651	0.87[CHB][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1949652	0.81[CHB][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1949653	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1949654	0.86[ASN][1000 genomes]
rs1976839	0.86[ASN][1000 genomes]
rs2030474	0.83[ASN][1000 genomes]
rs2049180	0.87[CHD][hapmap]
rs2090862	0.87[CHD][hapmap]
rs2103001	0.87[CHD][hapmap]
rs2139971	0.93[ASN][1000 genomes]
rs4233985	0.87[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs4350692	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs4375810	0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4580336	0.87[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs4638732	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs4672641	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672643	0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs4673654	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6718075	0.83[CHD][hapmap]
rs6724508	0.89[ASN][1000 genomes]
rs6727447	0.85[CHB][hapmap]
rs6727639	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6742273	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6745160	0.81[EUR][1000 genomes]
rs6755027	0.80[CHD][hapmap]
rs6755951	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7560301	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7561603	0.87[CHB][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7570768	0.81[CHB][hapmap]
rs7581138	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7592673	0.86[ASN][1000 genomes]
rs9288449	0.81[CHB][hapmap]
rs939224	0.87[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs939226	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs9653257	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:25 , 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
12	nsv460074	chr2:213114645-213151230	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	nsv584347	chr2:213114645-213151230	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
14	nsv834526	chr2:213114901-213237146	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
15	nsv834527	chr2:213115966-213334308	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1011111	chr2:213116621-213178740	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
17	nsv460075	chr2:213117976-213192660	Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
18	nsv584348	chr2:213117976-213192660	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
19	nsv584349	chr2:213117976-213200920	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
20	nsv460076	chr2:213120523-213165247	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
21	nsv584350	chr2:213120523-213165247	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
22	nsv875808	chr2:213120523-213183696	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
23	nsv460077	chr2:213122718-213165247	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
24	nsv584351	chr2:213122718-213165247	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
25	nsv875809	chr2:213122718-213221111	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1948875	FN1	cis	cerebellum	SCAN
rs1948875	VWC2L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:213107800-213134000	Weak transcription	Aorta	Aorta
2	chr2:213114600-213130400	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:213115400-213134000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:213121800-213122800	Enhancers	Brain Substantia Nigra	brain
5	chr2:213122400-213122800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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