Variant report

Variant	rs2066981
Chromosome Location	chr1:155172379-155172380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155171387-155173548	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:155172230-155172429	A549	lung:	n/a	n/a
3	POLR2A	chr1:155171689-155172668	PBDE	blood:	n/a	n/a
4	POLR2A	chr1:155171562-155172503	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:155169211-155173743	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr1:155172077-155172511	U87	brain:	n/a	n/a
7	POLR2A	chr1:155172112-155172404	U87	brain:	n/a	n/a
8	POLR2A	chr1:155169218-155173608	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr1:155171486-155173560	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr1:155170928-155173751	U87	brain:	n/a	n/a
11	POLR2A	chr1:155171327-155172737	K562	blood:	n/a	n/a
12	POLR2A	chr1:155169213-155174029	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr1:155170934-155173823	U87	brain:	n/a	n/a
14	POLR2A	chr1:155169187-155174183	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr1:155171690-155173583	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:155168973-155179742	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr1:155169109-155175268	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155169616..155173195-chr1:155194780..155198735,4	MCF-7	breast:
2	chr1:155169679..155172666-chr1:155186873..155189391,3	MCF-7	breast:
3	chr1:155171519..155180465-chr1:155194608..155199196,19	MCF-7	breast:

No data

Variant related genes	Relation type
THBS3	TF binding region
ENSG00000160766	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 21 )

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

rs_ID	r²[population]
rs10157801	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs1057941	0.80[ASN][1000 genomes]
rs10908458	0.83[CHB][hapmap]
rs11264337	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap]
rs11264338	0.83[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap]
rs11264339	0.83[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs12025371	0.83[CHB][hapmap]
rs12028043	0.83[CHB][hapmap];0.93[CHD][hapmap]
rs12407919	0.85[AFR][1000 genomes]
rs12411216	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12723761	0.81[AFR][1000 genomes]
rs12904	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs2049805	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2075569	0.85[AFR][1000 genomes]
rs2075570	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2075571	0.84[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs28445596	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2974929	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2974930	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2974931	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2974935	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2974937	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2990220	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2990245	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs370545	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754485	0.85[AFR][1000 genomes]
rs3768566	0.83[AFR][1000 genomes]
rs3814316	0.81[JPT][hapmap]
rs4072037	0.92[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4246529	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs4276913	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs4421576	0.83[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs4460629	0.85[ASW][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap]
rs4745	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs4971059	0.81[JPT][hapmap]
rs4971073	0.80[CHD][hapmap]
rs4971079	0.83[CHB][hapmap];0.93[CHD][hapmap]
rs4971085	0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap]
rs4971088	0.83[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs4971089	0.80[ASN][1000 genomes]
rs4971100	0.81[JPT][hapmap]
rs497829	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs734074	0.80[AFR][1000 genomes]
rs7556304	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap]
rs760077	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs914615	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9297	0.83[CHB][hapmap];0.89[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv464084	chr1:155082298-155194980	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS 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	366 gene(s)	inside rSNPs	diseases
4	nsv547961	chr1:155082298-155194980	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
5	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer 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	434 gene(s)	inside rSNPs	diseases
6	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
7	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers 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	452 gene(s)	inside rSNPs	diseases
8	nsv470741	chr1:155115260-155230131	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
9	nsv1010146	chr1:155119096-155201064	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
10	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
11	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
12	nsv872458	chr1:155146102-155180466	Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	316 gene(s)	inside rSNPs	diseases
13	nsv527682	chr1:155149718-155197462	Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	361 gene(s)	inside rSNPs	diseases
14	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs2066981	THBS3	cis	Whole Blood	GTEx
rs2066981	RP11-263K19.4	cis	Whole Blood	GTEx
rs2066981	GBAP1	cis	parietal	SCAN
rs2066981	IL6R	cis	lymphoblastoid	seeQTL
rs2066981	GBAP1	cis	Esophagus Muscularis	GTEx
rs2066981	THEM5	cis	parietal	SCAN
rs2066981	GBAP1	cis	Thyroid	GTEx
rs2066981	GBAP1	cis	Artery Aorta	GTEx
rs2066981	RP11-263K19.6	cis	Whole Blood	GTEx
rs2066981	GBAP1	cis	Adipose Subcutaneous	GTEx
rs2066981	SPRR4	cis	parietal	SCAN
rs2066981	YY1AP1	cis	cerebellum	SCAN
rs2066981	LASS2	cis	parietal	SCAN
rs2066981	GBAP1	cis	Artery Tibial	GTEx
rs2066981	GBAP1	cis	Esophagus Mucosa	GTEx
rs2066981	GBAP1	cis	Heart Left Ventricle	GTEx
rs2066981	IVL	cis	parietal	SCAN
rs2066981	GBAP1	cis	lung	GTEx
rs2066981	GBA	cis	Esophagus Mucosa	GTEx
rs2066981	GNAI2	trans	lymphoblastoid	RTeQTL
rs2066981	GBA///GBAP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155163600-155177400	Weak transcription	Small Intestine	intestine
2	chr1:155164800-155176800	Weak transcription	Primary T cells from cord blood	blood
3	chr1:155165000-155176600	Weak transcription	Liver	Liver
4	chr1:155165000-155176800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:155165400-155176600	Weak transcription	Brain Angular Gyrus	brain
6	chr1:155165400-155176800	Weak transcription	Right Atrium	heart
7	chr1:155165400-155176800	Weak transcription	Right Ventricle	heart
8	chr1:155165400-155177000	Weak transcription	Thymus	Thymus
9	chr1:155165600-155176600	Weak transcription	Fetal Kidney	kidney
10	chr1:155165600-155176600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:155165600-155176800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:155165600-155176800	Weak transcription	HMEC	breast
13	chr1:155165800-155176000	Strong transcription	Fetal Intestine Small	intestine
14	chr1:155165800-155176600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:155165800-155176800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:155166000-155172400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:155166000-155174800	Strong transcription	Placenta Amnion	Placenta Amnion
18	chr1:155166000-155176600	Weak transcription	Fetal Thymus	thymus
19	chr1:155166000-155176800	Weak transcription	K562	blood
20	chr1:155166200-155172400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:155166200-155174600	Weak transcription	Stomach Mucosa	stomach
22	chr1:155166200-155175000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:155166200-155175600	Strong transcription	Fetal Muscle Leg	muscle
24	chr1:155166400-155175600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:155166400-155175800	Strong transcription	Fetal Stomach	stomach
26	chr1:155166400-155176200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:155166600-155172400	Strong transcription	NHLF	lung
28	chr1:155166600-155173400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:155167000-155173200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr1:155167000-155173400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:155167000-155177200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:155167200-155176400	Weak transcription	Fetal Brain Male	brain
33	chr1:155167600-155175200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:155167800-155175000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:155168000-155173400	Strong transcription	Brain Anterior Caudate	brain
36	chr1:155168000-155174800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:155168200-155174800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:155168200-155174800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:155168200-155175200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr1:155168400-155172800	Weak transcription	Esophagus	oesophagus
41	chr1:155168400-155173600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:155168400-155174200	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr1:155168400-155174600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:155168400-155175200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:155168400-155176200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:155168400-155176200	Weak transcription	HSMM	muscle
47	chr1:155168400-155176600	Weak transcription	Adipose Nuclei	Adipose
48	chr1:155168400-155176600	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:155168400-155176600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:155168400-155176800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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