Variant report

Variant	rs6726061
Chromosome Location	chr2:210449349-210449350
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	chr2:210443684..210445464-chr2:210448136..210450654,2	K562	blood:

Variant related genes	Relation type
ENSG00000078018	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10172200	0.87[JPT][hapmap]
rs10196314	0.87[JPT][hapmap]
rs10196600	0.87[JPT][hapmap]
rs10198751	0.88[CEU][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs10206817	0.93[JPT][hapmap]
rs10490021	0.87[JPT][hapmap]
rs10932305	0.87[JPT][hapmap]
rs11692075	0.87[JPT][hapmap]
rs12613705	0.84[CHD][hapmap]
rs12614031	0.87[JPT][hapmap]
rs12615372	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12616589	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs12618080	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs12620654	0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12622979	0.92[ASN][1000 genomes]
rs12992342	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13385585	0.87[JPT][hapmap]
rs13419929	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1396779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509465	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1509468	0.88[JPT][hapmap]
rs1509469	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1509470	0.80[ASN][1000 genomes]
rs16843022	0.82[CEU][hapmap]
rs16843329	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs16843351	0.93[JPT][hapmap]
rs16843354	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs16843360	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs16843382	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs16843453	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs16843614	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs16843618	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs169636	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2048250	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2191910	0.87[JPT][hapmap]
rs2239552	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs2239553	0.87[JPT][hapmap]
rs2239672	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs2268042	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs2268044	0.87[JPT][hapmap]
rs2271252	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs2286849	0.86[JPT][hapmap]
rs2286850	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs2300154	0.87[JPT][hapmap]
rs2366112	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2663648	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2663649	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2663651	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2663653	0.90[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2663659	0.91[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2710474	0.91[ASN][1000 genomes]
rs2710475	0.89[ASN][1000 genomes]
rs2710477	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs2710479	0.82[JPT][hapmap]
rs2710482	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs2710486	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs288070	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs288071	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs288079	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs288081	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs288084	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs288087	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs288088	0.86[EUR][1000 genomes]
rs288094	0.93[ASW][hapmap];1.00[CEU][hapmap];0.81[LWK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs288096	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs34455059	0.89[ASN][1000 genomes]
rs34850994	0.89[ASN][1000 genomes]
rs35409969	0.89[ASN][1000 genomes]
rs3738935	0.88[CHD][hapmap];0.81[JPT][hapmap]
rs3754597	0.87[JPT][hapmap]
rs3768810	0.87[JPT][hapmap]
rs3768813	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs3768814	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs3768815	0.87[JPT][hapmap]
rs3768816	0.87[JPT][hapmap]
rs3768822	0.87[JPT][hapmap]
rs3768826	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs3768832	0.87[JPT][hapmap]
rs3768833	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs3768834	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs3768835	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs3820746	0.91[JPT][hapmap]
rs3820748	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs4673486	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs55911510	0.90[ASN][1000 genomes]
rs56023260	0.95[ASN][1000 genomes]
rs56677957	0.82[ASN][1000 genomes]
rs56775639	0.89[ASN][1000 genomes]
rs56853570	0.91[ASN][1000 genomes]
rs57781584	0.99[ASN][1000 genomes]
rs58636345	0.93[ASN][1000 genomes]
rs59032380	0.89[ASN][1000 genomes]
rs60138527	0.80[ASN][1000 genomes]
rs60359169	0.92[ASN][1000 genomes]
rs60497472	0.99[ASN][1000 genomes]
rs6709925	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs6717554	0.87[JPT][hapmap]
rs6720659	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs6724834	0.87[JPT][hapmap]
rs6733319	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.92[ASN][1000 genomes]
rs6746029	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs723683	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs73071071	0.91[ASN][1000 genomes]
rs73071085	0.91[ASN][1000 genomes]
rs741006	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs741007	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs7594601	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs906831	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9288410	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs962475	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs994862	0.87[JPT][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6726061	LANCL1	cis	cerebellum	SCAN
rs6726061	GPR1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210443600-210461000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:210444800-210456800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:210445400-210449600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:210446200-210456800	Weak transcription	Brain Anterior Caudate	brain
5	chr2:210446600-210461600	Weak transcription	Brain Angular Gyrus	brain
6	chr2:210446800-210449400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:210447800-210460400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:210448000-210449800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:210448200-210449600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:210448600-210452000	Enhancers	Fetal Brain Male	brain
11	chr2:210448800-210449600	Enhancers	Brain Cingulate Gyrus	brain
12	chr2:210448800-210450400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr2:210449000-210449600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:210449000-210449600	Enhancers	Fetal Brain Female	brain
15	chr2:210449000-210451200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:210449200-210451000	Weak transcription	Brain Germinal Matrix	brain

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