Variant report

Variant	rs35902489
Chromosome Location	chr3:100980849-100980850
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10451923	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10511189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1520654	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16843627	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16843634	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16843699	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16843817	1.00[CEU][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17487	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1986294	0.91[ASN][1000 genomes]
rs2271972	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2449822	0.96[ASN][1000 genomes]
rs2449823	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs3732893	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3773915	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3773917	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3773918	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4553955	1.00[CEU][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs475521	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs476090	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs476491	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs478173	0.95[ASN][1000 genomes]
rs479522	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs479723	0.96[ASN][1000 genomes]
rs481809	0.96[ASN][1000 genomes]
rs482055	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs482436	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs482976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs483947	0.93[ASN][1000 genomes]
rs485130	0.96[ASN][1000 genomes]
rs489455	0.91[ASN][1000 genomes]
rs500480	0.93[ASN][1000 genomes]
rs501702	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs505037	0.93[ASN][1000 genomes]
rs513188	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs513994	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs515307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs516312	0.96[ASN][1000 genomes]
rs517698	0.91[ASN][1000 genomes]
rs520879	1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[ASN][1000 genomes]
rs522749	0.84[ASN][1000 genomes]
rs527836	0.96[ASN][1000 genomes]
rs530566	0.93[ASN][1000 genomes]
rs535881	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs536561	0.96[ASN][1000 genomes]
rs538834	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs545322	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs546090	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs550241	0.93[ASN][1000 genomes]
rs554215	0.91[ASN][1000 genomes]
rs559042	0.93[ASN][1000 genomes]
rs559400	0.90[ASN][1000 genomes]
rs563909	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs567983	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs569339	0.93[ASN][1000 genomes]
rs570318	0.91[ASN][1000 genomes]
rs571883	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs573908	0.91[ASN][1000 genomes]
rs575317	0.91[ASN][1000 genomes]
rs62280607	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62280609	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62280631	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62280633	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62280636	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62280637	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62280663	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62280664	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62280665	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62280669	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62280670	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62280671	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62280673	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62280674	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62280675	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62280719	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62280720	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62280721	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62280722	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62280725	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62280726	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62280728	0.83[EUR][1000 genomes]
rs62280731	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62280733	0.83[EUR][1000 genomes]
rs62280735	0.83[EUR][1000 genomes]
rs62280737	0.83[EUR][1000 genomes]
rs62282871	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282872	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62282873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282875	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62282885	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62282886	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62282887	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62282888	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62282889	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62282890	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62282892	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6441595	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6796058	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6798685	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs693428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs72932462	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611378	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7621506	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7622461	0.83[EUR][1000 genomes]
rs7632064	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7634592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9790303	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv877222	chr3:100715576-101038297	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2754039	chr3:100882310-100981310	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3439278	chr3:100936513-101162102	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35902489	NIT2	cis	cerebellum	SCAN
rs35902489	ST3GAL6	cis	parietal	SCAN
rs35902489	ZBTB11	cis	cerebellum	SCAN
rs35902489	CBLB	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100954800-100992600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr3:100955000-100994000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr3:100958800-101012800	Weak transcription	Left Ventricle	heart
4	chr3:100973800-100990600	Weak transcription	Primary T cells from cord blood	blood
5	chr3:100975400-100997800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:100976600-100981200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:100979600-100982000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:100979600-100982200	Enhancers	HSMMtube	muscle
9	chr3:100979600-100995000	Weak transcription	Aorta	Aorta
10	chr3:100979800-100981000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:100979800-100981000	Enhancers	Osteobl	bone
12	chr3:100980000-100981000	Weak transcription	Brain Angular Gyrus	brain
13	chr3:100980000-100981200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:100980000-100981200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr3:100980200-100982400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:100980400-100981000	Enhancers	NHDF-Ad	bronchial
17	chr3:100980800-100982800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:100980800-100998000	Weak transcription	HSMM	muscle

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