Variant report

Variant	rs34103461
Chromosome Location	chr2:183316191-183316192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10178586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10207132	1.00[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs10497598	0.94[CEU][hapmap]
rs10497600	1.00[CEU][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10497601	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10497602	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10497603	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs1125184	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11686025	0.88[CEU][hapmap]
rs12465662	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[ASN][1000 genomes]
rs12465755	0.86[ASN][1000 genomes]
rs12466618	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs12466937	0.86[ASN][1000 genomes]
rs12468232	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs12468346	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs12470124	0.83[ASN][1000 genomes]
rs12473820	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12478132	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs12479259	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs13407156	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13417404	0.84[CHD][hapmap]
rs1346775	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs1367203	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1367204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1430147	0.94[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs1430148	0.94[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs1430160	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1583112	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs1583114	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16823233	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16823254	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16823257	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16823275	0.81[ASN][1000 genomes]
rs17265027	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17265061	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17265189	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs17356152	0.85[CEU][hapmap]
rs17356166	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17356207	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17356214	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17356296	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs17356303	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs17356331	0.80[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap]
rs1946815	0.85[CEU][hapmap]
rs28569979	0.88[EUR][1000 genomes]
rs34744930	0.86[ASN][1000 genomes]
rs35809203	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4318355	0.90[AFR][1000 genomes]
rs4496292	0.90[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs4572561	1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs4666582	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4666585	0.86[ASN][1000 genomes]
rs4666835	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4666836	0.84[CHD][hapmap]
rs4666837	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4666840	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4666841	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap]
rs62188260	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62188266	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62188267	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62188268	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62188269	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62188270	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62188283	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62188284	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62188286	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62188287	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62188288	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62188289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62188290	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62188294	0.89[ASN][1000 genomes]
rs62188295	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs62188296	0.91[ASN][1000 genomes]
rs62188297	0.91[ASN][1000 genomes]
rs62189024	0.91[ASN][1000 genomes]
rs62189025	0.84[ASN][1000 genomes]
rs62189027	0.86[ASN][1000 genomes]
rs62190201	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62190677	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs62190684	0.81[ASN][1000 genomes]
rs6760364	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533782	chr2:183059730-183500040	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv834481	chr2:183189758-183339577	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv2830429	chr2:183300759-183545378	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3323574	chr2:183315057-183317155	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
6	esv2479479	chr2:183315368-183316896	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
7	esv3322767	chr2:183315607-183316605	Weak transcription	n/a	n/a	inside rSNPs	diseases
8	esv2241730	chr2:183315617-183316309	Weak transcription	n/a	n/a	inside rSNPs	diseases
9	esv3458818	chr2:183315687-183316215	Weak transcription	n/a	n/a	inside rSNPs	diseases
10	esv3514656	chr2:183315706-183316224	Weak transcription	n/a	n/a	inside rSNPs	diseases
11	esv3514660	chr2:183315709-183316228	Weak transcription	n/a	n/a	inside rSNPs	diseases
12	esv7845	chr2:183315731-183316385	Weak transcription	n/a	n/a	inside rSNPs	diseases
13	esv3458817	chr2:183315743-183316191	Weak transcription	n/a	n/a	inside rSNPs	diseases
14	esv3458821	chr2:183315750-183316192	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34103461	SSFA2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183298800-183320800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:183313000-183321400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:183313000-183342600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:183313800-183320800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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