Variant report

Variant	rs3821546
Chromosome Location	chr3:139171328-139171329
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	chr3:139165019..139166769-chr3:139169234..139171368,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1007079	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11919679	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924964	0.87[CEU][hapmap]
rs12107249	0.87[CEU][hapmap]
rs1599926	0.87[CEU][hapmap]
rs1602627	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1610195	0.80[MEX][hapmap];0.80[MKK][hapmap]
rs182409	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs188419	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs192688	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211581	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs211584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2233817	0.94[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278577	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2307030	1.00[CEU][hapmap]
rs295475	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs295476	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs295477	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3772874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772875	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60082560	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60961550	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439863	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6776315	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72986799	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7373142	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7373302	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7648636	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649535	0.87[CEU][hapmap]
rs7651618	0.87[CEU][hapmap]
rs9819224	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9858740	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9859683	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9879736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9879748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9882253	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1000519	chr3:139159300-139206245	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2752377	chr3:139163302-139188302	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3821546	ESYT3	cis	cerebellum	SCAN
rs3821546	IL20RB	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139142200-139172200	Weak transcription	Fetal Heart	heart
2	chr3:139142800-139176800	Weak transcription	Fetal Stomach	stomach
3	chr3:139144800-139173200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:139154200-139173600	Weak transcription	Ovary	ovary
5	chr3:139154200-139178600	Weak transcription	Left Ventricle	heart
6	chr3:139158600-139172600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:139158600-139174800	Weak transcription	Adipose Nuclei	Adipose
8	chr3:139160200-139174800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:139160600-139174800	Weak transcription	Fetal Brain Male	brain
10	chr3:139163400-139189000	Weak transcription	Small Intestine	intestine
11	chr3:139163800-139180200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:139165800-139178600	Weak transcription	Right Ventricle	heart
13	chr3:139166000-139179000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:139167000-139175400	Weak transcription	Fetal Brain Female	brain
15	chr3:139167400-139173200	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:139167400-139174800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:139167400-139176000	Weak transcription	Brain Anterior Caudate	brain
18	chr3:139167600-139173400	Weak transcription	Brain Germinal Matrix	brain
19	chr3:139168000-139175200	Weak transcription	Brain Angular Gyrus	brain
20	chr3:139168600-139196000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:139169200-139172200	Enhancers	HSMMtube	muscle
22	chr3:139169200-139175000	Genic enhancers	Fetal Intestine Small	intestine
23	chr3:139169400-139173400	Weak transcription	Pancreas	Pancrea
24	chr3:139170200-139171400	Enhancers	Brain Cingulate Gyrus	brain
25	chr3:139170200-139172000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:139170200-139173000	Genic enhancers	Fetal Intestine Large	intestine
27	chr3:139170600-139171400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr3:139170600-139171800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:139170600-139171800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:139170600-139172200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:139170600-139172400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:139170600-139173200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr3:139170800-139172400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:139170800-139173600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:139170800-139174600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:139171200-139171400	Enhancers	Brain Substantia Nigra	brain
37	chr3:139171200-139171400	Genic enhancers	Duodenum Mucosa	Duodenum
38	chr3:139171200-139171400	Enhancers	Right Atrium	heart
39	chr3:139171200-139210200	Weak transcription	Stomach Smooth Muscle	stomach

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