Variant report

Variant	rs10874471
Chromosome Location	chr2:96038093-96038094
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11164125	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11677429	0.86[JPT][hapmap];0.82[YRI][hapmap]
rs11897976	0.95[MEX][hapmap];0.83[AMR][1000 genomes]
rs12468117	0.90[JPT][hapmap]
rs12468777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471472	0.86[JPT][hapmap];0.82[YRI][hapmap]
rs1364394	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs1559483	0.89[YRI][hapmap]
rs1862897	0.95[MEX][hapmap];0.84[AMR][1000 genomes]
rs2042477	0.84[AMR][1000 genomes]
rs2113417	0.95[MEX][hapmap];0.84[AMR][1000 genomes]
rs2113419	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2320431	0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3755518	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3755519	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3755520	0.95[MEX][hapmap]
rs3755523	0.95[MEX][hapmap]
rs3772031	1.00[ASW][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3772032	1.00[ASW][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3772033	1.00[ASW][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3772041	0.95[MEX][hapmap]
rs3772042	0.95[MEX][hapmap]
rs3772044	0.95[MEX][hapmap]
rs3821341	0.83[AMR][1000 genomes]
rs4283455	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4854251	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854253	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs58610630	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61649840	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6577012	0.95[MEX][hapmap]
rs6577013	0.87[ASW][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs6715813	0.95[MEX][hapmap]
rs6741001	0.84[AMR][1000 genomes]
rs6750542	0.83[AMR][1000 genomes]
rs67628541	0.93[ASN][1000 genomes]
rs72821422	0.93[ASN][1000 genomes]
rs7574862	0.91[MEX][hapmap]
rs7580685	0.95[MEX][hapmap]
rs7602807	0.84[AMR][1000 genomes]
rs869185	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs870393	0.95[MEX][hapmap]
rs889851	0.95[MEX][hapmap]
rs889852	0.95[MEX][hapmap]
rs918811	0.95[MEX][hapmap];0.84[AMR][1000 genomes]
rs954078	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs9678800	1.00[ASW][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9989786	0.95[MEX][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv817299	chr2:95799814-96159275	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv998370	chr2:95897299-96074071	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv535823	chr2:95897299-96074071	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv998014	chr2:95913278-96296630	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv528011	chr2:95931218-96057011	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010831	chr2:95935648-96074213	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv535824	chr2:95935648-96074213	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv2757818	chr2:95970138-96152559	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv2759076	chr2:95970138-96152559	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv998543	chr2:95979772-96074212	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv535825	chr2:95979772-96074212	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10874471	KCNIP3	cis	cerebellum	SCAN
rs10874471	KCNIP3	cis	Thyroid	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96014200-96041400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:96021200-96039800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:96025600-96038800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:96025600-96039600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:96025600-96042400	Weak transcription	Ovary	ovary
6	chr2:96025800-96039400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:96025800-96039600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:96030400-96040600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:96030400-96054600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:96034000-96045400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:96035600-96042800	Weak transcription	Aorta	Aorta
12	chr2:96036400-96042200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:96036600-96042800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:96036600-96054800	Weak transcription	Brain Angular Gyrus	brain
15	chr2:96037200-96042400	Weak transcription	Fetal Brain Female	brain
16	chr2:96037400-96040600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:96038000-96038800	ZNF genes & repeats	Spleen	Spleen
18	chr2:96038000-96039600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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