Variant report

Variant	rs2071803
Chromosome Location	chr3:50407344-50407345
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50407312-50407389	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50405624..50407617-chr3:50410447..50413698,3	K562	blood:
2	chr3:50395602..50397170-chr3:50405064..50407800,2	MCF-7	breast:
3	chr3:50407190..50409972-chr3:50577719..50580221,2	K562	blood:
4	chr3:50395175..50398568-chr3:50405872..50408307,3	K562	blood:
5	chr3:50406050..50408278-chr3:50414386..50416245,2	MCF-7	breast:
6	chr3:50407329..50410054-chr3:50589199..50591435,2	K562	blood:

No data

Variant related genes	Relation type
CACNA2D2	TF binding region
ENSG00000126062	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10510755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12629572	1.00[CEU][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs12635953	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1989839	1.00[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs2071802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2073498	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073499	0.93[CEU][hapmap]
rs2097247	0.92[ASN][1000 genomes]
rs2233474	0.93[CEU][hapmap]
rs2236939	0.86[CEU][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap]
rs2236950	1.00[ASW][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs2236967	1.00[ASW][hapmap]
rs2236968	1.00[ASW][hapmap]
rs2236988	1.00[ASW][hapmap]
rs2239801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282756	1.00[ASW][hapmap]
rs2301639	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[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28365992	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3755832	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3806708	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs41291724	0.92[ASN][1000 genomes]
rs4141060	0.93[CEU][hapmap]
rs45536634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57319506	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57462170	0.82[EUR][1000 genomes]
rs57838764	0.82[EUR][1000 genomes]
rs58051625	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60247651	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6776145	1.00[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs762898	1.00[ASW][hapmap]
rs7642692	0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
7	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
9	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
10	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
11	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
12	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
13	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
14	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
15	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
16	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
17	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
18	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2071803	SLC25A20	cis	cerebellum	SCAN
rs2071803	NEK4	cis	parietal	SCAN
rs2071803	TRAIP	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50403200-50408000	Weak transcription	Brain Angular Gyrus	brain
2	chr3:50403200-50408000	Weak transcription	Fetal Heart	heart
3	chr3:50403200-50408400	Weak transcription	Fetal Lung	lung
4	chr3:50403200-50417200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:50403400-50408000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:50403400-50408000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:50403400-50408400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:50403400-50410000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:50403600-50408400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:50403800-50408400	Weak transcription	Fetal Stomach	stomach
11	chr3:50403800-50409600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:50403800-50409600	Weak transcription	Fetal Intestine Small	intestine
13	chr3:50403800-50409800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:50403800-50409800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:50403800-50410000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:50404000-50409400	Weak transcription	Fetal Thymus	thymus
17	chr3:50404000-50409800	Weak transcription	Thymus	Thymus
18	chr3:50404200-50408000	Weak transcription	Fetal Brain Female	brain
19	chr3:50404200-50410600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:50404400-50407400	Weak transcription	Brain Germinal Matrix	brain
21	chr3:50404600-50409800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr3:50404600-50410000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:50404600-50415400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:50404800-50407400	Weak transcription	Pancreas	Pancrea
25	chr3:50405000-50409800	Weak transcription	Primary T cells from cord blood	blood
26	chr3:50405000-50416400	Weak transcription	Gastric	stomach
27	chr3:50405200-50407400	Weak transcription	Lung	lung
28	chr3:50405200-50409800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:50405600-50409800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:50405600-50410000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:50405800-50411200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:50406000-50411000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr3:50406800-50407600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:50406800-50409800	Weak transcription	Spleen	Spleen
35	chr3:50407000-50407400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:50407000-50407600	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:50407000-50408000	Weak transcription	K562	blood
38	chr3:50407200-50407400	Bivalent Enhancer	Placenta	Placenta
39	chr3:50407200-50410600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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