Variant report

Variant	rs2073498
Chromosome Location	chr3:50369546-50369547
allele	A/C
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	POLR2A	chr3:50368542-50370309	HL-60	blood:	n/a	n/a
2	POLR2A	chr3:50369375-50369990	GM12892	blood:	n/a	n/a
3	POLR2A	chr3:50368806-50369848	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:50369316-50370060	HL-60	blood:	n/a	n/a
5	POLR2A	chr3:50369372-50369762	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:50368590-50370077	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:50368961-50370060	GM12892	blood:	n/a	n/a
8	POLR2A	chr3:50368769-50369877	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:50369388-50369823	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr3:50369425-50372280	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:50369336-50370000	K562	blood:	n/a	n/a
12	POLR2A	chr3:50369511-50369901	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:50365500-50370094	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50268765..50270756-chr3:50367909..50369818,2	K562	blood:

Variant related genes	Relation type
TUSC2	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10510755	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12629572	0.93[CEU][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs12635953	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1989839	0.93[CEU][hapmap];0.86[GIH][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs2071802	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071803	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	0.87[CEU][hapmap]
rs2097247	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2233474	0.87[CEU][hapmap]
rs2236939	0.81[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs2236950	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap]
rs2236967	1.00[ASW][hapmap]
rs2236968	1.00[ASW][hapmap]
rs2236988	1.00[ASW][hapmap]
rs2239801	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282756	1.00[ASW][hapmap]
rs2301639	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[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526392	0.90[GIH][hapmap]
rs2526394	0.90[GIH][hapmap]
rs2526395	0.90[GIH][hapmap]
rs2526396	0.90[GIH][hapmap]
rs2624837	0.90[GIH][hapmap]
rs2624842	0.90[GIH][hapmap]
rs28365992	1.00[ASW][hapmap];0.93[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3755832	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3806708	1.00[ASW][hapmap];0.93[CEU][hapmap];0.90[GIH][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41291724	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4141060	0.87[CEU][hapmap]
rs45536634	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57319506	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57462170	0.85[EUR][1000 genomes]
rs57838764	0.85[EUR][1000 genomes]
rs58051625	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60247651	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6776145	0.93[CEU][hapmap];0.86[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs762898	1.00[ASW][hapmap]
rs7642692	0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:23 , 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	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
10	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
11	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
12	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	nsv590257	chr3:50302830-50393640	Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
17	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
18	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
19	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
20	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
21	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
22	nsv590258	chr3:50368278-50381022	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
23	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2073498	NEK4	cis	parietal	SCAN
rs2073498	TRAIP	cis	parietal	SCAN
rs2073498	SLC25A20	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50366000-50374000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:50366200-50370600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:50366200-50370800	Strong transcription	HSMM	muscle
4	chr3:50366200-50371200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:50366400-50369600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:50366400-50369600	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:50366400-50370600	Weak transcription	Fetal Heart	heart
8	chr3:50366400-50370600	Weak transcription	Right Atrium	heart
9	chr3:50366400-50371200	Strong transcription	Fetal Stomach	stomach
10	chr3:50366600-50369600	Strong transcription	Fetal Muscle Trunk	muscle
11	chr3:50366600-50370600	Strong transcription	Fetal Intestine Small	intestine
12	chr3:50366600-50370800	Strong transcription	Fetal Thymus	thymus
13	chr3:50366600-50371800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:50366800-50369600	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr3:50366800-50369600	Strong transcription	Primary hematopoietic stem cells	blood
16	chr3:50366800-50369600	Strong transcription	Aorta	Aorta
17	chr3:50366800-50369600	Strong transcription	Liver	Liver
18	chr3:50366800-50369600	Strong transcription	Brain Cingulate Gyrus	brain
19	chr3:50366800-50369600	Strong transcription	Pancreas	Pancrea
20	chr3:50366800-50369600	Strong transcription	NH-A	brain
21	chr3:50366800-50369800	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr3:50366800-50369800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:50366800-50369800	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:50366800-50369800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:50366800-50369800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr3:50366800-50369800	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr3:50366800-50369800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:50366800-50369800	Strong transcription	Colon Smooth Muscle	Colon
29	chr3:50366800-50369800	Strong transcription	Fetal Brain Female	brain
30	chr3:50366800-50369800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr3:50366800-50369800	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:50366800-50370000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:50366800-50370000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:50366800-50370000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:50366800-50370000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:50366800-50370000	Strong transcription	Adipose Nuclei	Adipose
37	chr3:50366800-50370000	Strong transcription	Esophagus	oesophagus
38	chr3:50366800-50370200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:50366800-50370200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:50366800-50370200	Strong transcription	Fetal Intestine Large	intestine
41	chr3:50366800-50370200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr3:50366800-50370400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:50366800-50370400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:50366800-50370600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:50366800-50370600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:50366800-50370600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:50366800-50370600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr3:50366800-50370600	Strong transcription	Fetal Muscle Leg	muscle
49	chr3:50366800-50370600	Strong transcription	Placenta	Placenta
50	chr3:50366800-50370600	Strong transcription	Lung	lung

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