Variant report

Variant	rs1476876
Chromosome Location	chr2:210646449-210646450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10182553	0.88[ASN][1000 genomes]
rs10183590	0.81[EUR][1000 genomes]
rs10183604	0.81[EUR][1000 genomes]
rs10490021	0.81[EUR][1000 genomes]
rs10490022	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804176	0.85[EUR][1000 genomes]
rs10932305	0.85[EUR][1000 genomes]
rs10932306	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11674672	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11674950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677476	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11677489	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11677975	0.81[EUR][1000 genomes]
rs11678044	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11679862	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11680007	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680964	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11682692	0.81[EUR][1000 genomes]
rs11687043	0.88[EUR][1000 genomes]
rs11689771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11692345	0.88[EUR][1000 genomes]
rs11692608	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693202	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11884376	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11887161	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898077	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11900602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12105654	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12105660	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12613705	0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs12614031	0.81[EUR][1000 genomes]
rs12615516	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12616589	0.81[JPT][hapmap]
rs12619203	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12619253	0.81[EUR][1000 genomes]
rs12619409	0.85[EUR][1000 genomes]
rs12622305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509468	0.81[JPT][hapmap]
rs1509469	0.81[JPT][hapmap]
rs16843421	0.81[EUR][1000 genomes]
rs16843453	0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs16843515	0.81[EUR][1000 genomes]
rs16843544	0.85[EUR][1000 genomes]
rs16843614	0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs16843618	0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs16843626	0.85[EUR][1000 genomes]
rs2098204	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2215624	0.88[EUR][1000 genomes]
rs2215625	0.88[EUR][1000 genomes]
rs2239553	0.85[EUR][1000 genomes]
rs2239672	0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs2268042	0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs2284360	0.85[EUR][1000 genomes]
rs2300154	0.85[EUR][1000 genomes]
rs2710477	0.92[JPT][hapmap]
rs35337581	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35872449	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3754597	0.85[EUR][1000 genomes]
rs3768810	0.81[EUR][1000 genomes]
rs3768813	0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs3768814	0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs3768826	0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs3768835	0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs3820746	0.82[EUR][1000 genomes]
rs3886931	0.81[EUR][1000 genomes]
rs4672559	0.85[EUR][1000 genomes]
rs56825045	0.85[EUR][1000 genomes]
rs57305145	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57542539	0.85[EUR][1000 genomes]
rs57637604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57853945	0.85[EUR][1000 genomes]
rs57990979	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58248939	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58295121	0.85[EUR][1000 genomes]
rs58525719	0.85[EUR][1000 genomes]
rs58779755	0.85[EUR][1000 genomes]
rs59155421	0.81[EUR][1000 genomes]
rs59555743	0.85[EUR][1000 genomes]
rs60161291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60640585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61333809	0.85[EUR][1000 genomes]
rs61356588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61420319	0.85[EUR][1000 genomes]
rs6716831	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6720659	0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs6742314	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73074733	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73074750	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73074751	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73074763	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73074778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73074779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73074784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73074787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73074791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73074801	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73076704	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73076710	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs741006	0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs7564369	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7569393	0.85[EUR][1000 genomes]
rs7594601	0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs7595017	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs975551	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1009129	chr2:210550858-210681136	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv963889	chr2:210645653-210651831	Weak transcription Strong transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1476876	LANCL1	cis	lymphoblastoid	seeQTL
rs1476876	SLC44A2	trans	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210637600-210653800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:210638200-210661400	Weak transcription	Fetal Brain Female	brain
3	chr2:210638400-210651800	Weak transcription	Brain Angular Gyrus	brain
4	chr2:210638400-210652200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:210638400-210660000	Weak transcription	Fetal Brain Male	brain
6	chr2:210640400-210646600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:210640600-210648200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:210643800-210647400	Strong transcription	Brain Anterior Caudate	brain
9	chr2:210643800-210655800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:210644400-210650600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:210644400-210655800	Weak transcription	Brain Germinal Matrix	brain
12	chr2:210646000-210652400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:210646000-210656600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:210646400-210654600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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