Variant report

Variant	rs1415946
Chromosome Location	chr6:101846343-101846344
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr6:101846284-101847726	H1-neurons	neurons:	n/a	chr6:101846883-101846896 chr6:101847549-101847562
2	MXI1	chr6:101845906-101852010	SK-N-SH	brain:	n/a	chr6:101849846-101849861 chr6:101849844-101849859

Variant related genes	Relation type
GRIK2	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1475916	1.00[JPT][hapmap]
rs2518226	1.00[JPT][hapmap]
rs2518228	1.00[JPT][hapmap]
rs2518231	1.00[JPT][hapmap]
rs2518234	1.00[JPT][hapmap]
rs2518235	1.00[JPT][hapmap]
rs2518238	1.00[JPT][hapmap]
rs2518249	1.00[JPT][hapmap]
rs2579933	1.00[JPT][hapmap]
rs2579934	1.00[JPT][hapmap]
rs2788276	1.00[JPT][hapmap]
rs283227	0.84[ASN][1000 genomes]
rs283229	0.84[ASN][1000 genomes]
rs2852499	0.86[EUR][1000 genomes]
rs2852501	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852503	0.81[CEU][hapmap];1.00[GIH][hapmap]
rs2852507	0.81[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap]
rs2852508	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];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852509	0.87[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2852511	1.00[GIH][hapmap]
rs2852512	0.87[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2852532	1.00[JPT][hapmap]
rs3811080	1.00[JPT][hapmap]
rs485947	0.84[ASN][1000 genomes]
rs550690	0.84[ASN][1000 genomes]
rs5878658	0.96[ASN][1000 genomes]
rs597750	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs649828	0.84[ASN][1000 genomes]
rs683830	0.84[ASN][1000 genomes]
rs71566372	0.96[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	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101842200-101846600	Weak transcription	Pancreas	Pancrea
2	chr6:101842200-101849600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:101842400-101849600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:101842800-101846800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:101843200-101846400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:101843200-101846600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:101843200-101846800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:101843600-101846400	Weak transcription	Right Atrium	heart
9	chr6:101845200-101846400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:101846000-101846800	Active TSS	Brain Angular Gyrus	brain
11	chr6:101846000-101849600	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr6:101846200-101846600	Active TSS	Fetal Brain Female	brain
13	chr6:101846200-101847200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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