Variant report

Variant	rs1394780
Chromosome Location	chr2:213283190-213283191
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:213280702..213283541-chr2:213286415..213289040,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10166403	0.84[YRI][hapmap]
rs10167244	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10181082	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10188926	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10194540	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10197215	0.84[ASN][1000 genomes]
rs10202760	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs11894208	0.86[JPT][hapmap]
rs13383863	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13388956	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13393577	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13400881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13413335	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs13417523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1351593	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs1505368	0.86[JPT][hapmap]
rs16848753	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2178575	0.86[JPT][hapmap]
rs2178576	0.86[JPT][hapmap]
rs4404217	0.86[JPT][hapmap]
rs56041970	1.00[ASN][1000 genomes]
rs6435708	0.84[JPT][hapmap]
rs6435709	0.86[JPT][hapmap]
rs6712295	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6756468	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[ASN][1000 genomes]
rs6761143	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs7561571	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs7565257	1.00[JPT][hapmap]
rs7571561	0.86[JPT][hapmap]
rs7573568	0.86[JPT][hapmap]
rs7598042	1.00[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1014680	chr2:213142147-213301614	Weak transcription Enhancers 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
3	nsv1004573	chr2:213186537-213365252	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv875811	chr2:213200920-213347104	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1003694	chr2:213216431-213290523	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv2763101	chr2:213248318-213290535	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1394780	LANCL1	cis	parietal	SCAN
rs1394780	PRH1	trans	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:213280000-213284800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:213281000-213285200	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:213281600-213286200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:213282400-213283200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:213282400-213285200	Weak transcription	Brain Anterior Caudate	brain
6	chr2:213282400-213287000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:213282800-213286200	Weak transcription	Brain Angular Gyrus	brain
8	chr2:213283000-213284200	Weak transcription	Brain Substantia Nigra	brain

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