Variant report

Variant	rs6709925
Chromosome Location	chr2:210549474-210549475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 142 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10165558	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10169017	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10172200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10183590	0.98[ASN][1000 genomes]
rs10183604	0.98[ASN][1000 genomes]
rs10189911	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10193321	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10196314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10196600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10198751	0.85[JPT][hapmap]
rs10206817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10490021	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10804176	0.98[ASN][1000 genomes]
rs10932305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11677975	0.98[ASN][1000 genomes]
rs11682692	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11687043	0.95[ASN][1000 genomes]
rs11691800	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691894	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11692075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11692345	0.95[ASN][1000 genomes]
rs12613705	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.98[ASN][1000 genomes]
rs12614031	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12615372	0.87[JPT][hapmap]
rs12616589	0.82[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs12618080	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12619253	0.98[ASN][1000 genomes]
rs12619409	0.98[ASN][1000 genomes]
rs12620654	0.87[JPT][hapmap]
rs13385585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13409134	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419929	0.93[JPT][hapmap]
rs13422521	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13423127	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1509465	0.87[JPT][hapmap]
rs1509468	0.92[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs1509469	0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1509470	0.80[ASN][1000 genomes]
rs16843329	0.85[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs16843351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16843354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16843360	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16843382	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16843421	0.98[ASN][1000 genomes]
rs16843453	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16843515	0.98[ASN][1000 genomes]
rs16843544	0.98[ASN][1000 genomes]
rs16843614	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16843618	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16843626	0.98[ASN][1000 genomes]
rs16843651	0.98[ASN][1000 genomes]
rs2048250	0.87[JPT][hapmap]
rs2191910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2215624	0.98[ASN][1000 genomes]
rs2215625	0.89[ASN][1000 genomes]
rs2239552	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2239553	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2239672	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2268042	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2268044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2268045	0.98[ASN][1000 genomes]
rs2271252	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2284359	0.98[ASN][1000 genomes]
rs2284360	0.98[ASN][1000 genomes]
rs2286849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286850	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2300154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2366112	0.87[JPT][hapmap]
rs2663647	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2663648	0.87[JPT][hapmap]
rs2663649	0.85[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2663651	0.85[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2663653	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2663658	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2663659	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs2710477	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2710479	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2710480	0.86[ASN][1000 genomes]
rs2710482	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2710486	0.87[JPT][hapmap]
rs28435689	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28666486	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28758270	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288079	0.80[JPT][hapmap]
rs288081	0.80[JPT][hapmap]
rs288087	0.80[JPT][hapmap]
rs3738935	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3768810	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3768811	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768813	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3768814	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3768815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768820	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768821	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3768823	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768826	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3768827	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768828	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768830	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768833	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768834	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768835	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3820746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3820748	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3886931	0.98[ASN][1000 genomes]
rs4673486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56659802	0.95[ASN][1000 genomes]
rs56825045	0.98[ASN][1000 genomes]
rs57542539	0.98[ASN][1000 genomes]
rs57853945	0.98[ASN][1000 genomes]
rs58295121	0.97[ASN][1000 genomes]
rs58525719	0.98[ASN][1000 genomes]
rs58779755	0.93[ASN][1000 genomes]
rs59155421	1.00[ASN][1000 genomes]
rs59555743	0.98[ASN][1000 genomes]
rs60138527	0.80[ASN][1000 genomes]
rs60528820	0.84[AMR][1000 genomes]
rs61333809	0.98[ASN][1000 genomes]
rs61420319	0.98[ASN][1000 genomes]
rs6717554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6720659	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6724834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726061	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs6733319	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs6742314	0.88[MEX][hapmap]
rs6746029	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6761179	0.81[TSI][hapmap]
rs723683	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs741006	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs741007	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7567257	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7594601	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7596811	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs906831	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs9288410	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs962475	0.85[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs994862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875765	chr2:210537660-210618203	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6709925	LANCL1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210528600-210550200	Weak transcription	Brain Substantia Nigra	brain
2	chr2:210528800-210550200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:210531400-210587800	Weak transcription	Brain Angular Gyrus	brain
4	chr2:210536600-210552200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:210537000-210550400	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:210537000-210596800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:210537600-210550200	Weak transcription	Fetal Brain Male	brain
8	chr2:210540200-210552200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:210541600-210550600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:210541800-210551600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:210541800-210596400	Weak transcription	Gastric	stomach
12	chr2:210542000-210555400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:210543600-210552200	Weak transcription	Pancreas	Pancrea
14	chr2:210543800-210550200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:210544000-210550200	Weak transcription	Brain Anterior Caudate	brain
16	chr2:210544000-210596600	Weak transcription	Ovary	ovary
17	chr2:210544200-210555200	Weak transcription	Left Ventricle	heart
18	chr2:210544400-210598600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:210546200-210552400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:210546400-210550400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:210546400-210551800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:210546400-210552000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:210546400-210554800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:210546800-210560000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:210547600-210552200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:210547800-210551600	Weak transcription	Brain Germinal Matrix	brain
27	chr2:210547800-210552200	Weak transcription	Aorta	Aorta
28	chr2:210548400-210550400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:210549000-210549600	Strong transcription	Fetal Brain Female	brain
30	chr2:210549000-210551000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
31	chr2:210549200-210559600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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