Variant report

Variant	rs1109027
Chromosome Location	chr2:63815206-63815207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:173)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:173 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:63815063-63816553	GM19193	blood:	n/a	n/a
2	MAX	chr2:63815201-63816356	H1-hESC	embryonic stem cell:	n/a	n/a
3	NR2C2	chr2:63815203-63816548	Hela-S3	cervix:	n/a	chr2:63815660-63815669
4	TAF1	chr2:63815195-63816401	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:63815114-63816636	GM12892	blood:	n/a	n/a
6	GABPA	chr2:63814993-63816607	HL-60	blood:	n/a	n/a
7	GABPA	chr2:63815110-63816396	K562	blood:	n/a	n/a
8	HDAC2	chr2:63815118-63816322	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:63814866-63817603	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:63815163-63817205	H1-neurons	neurons:	n/a	n/a
11	RUNX3	chr2:63815146-63816718	GM12878	blood:	n/a	n/a
12	GABPA	chr2:63814826-63816834	MCF-7	breast:	n/a	n/a
13	POLR2A	chr2:63815144-63815523	GM12892	blood:	n/a	n/a
14	POLR2A	chr2:63815151-63816661	PFSK-1	brain:	n/a	n/a
15	CREB1	chr2:63815122-63816334	A549	lung:	n/a	n/a
16	RELA	chr2:63815183-63816835	GM12891	blood:	n/a	n/a
17	CREB1	chr2:63815203-63816705	HepG2	liver:	n/a	n/a
18	POLR2A	chr2:63815173-63816420	GM12878	blood:	n/a	n/a
19	MAX	chr2:63814875-63816947	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr2:63815150-63816557	K562	blood:	n/a	n/a
21	POLR2A	chr2:63815204-63816538	HepG2	liver:	n/a	n/a
22	NR2C2	chr2:63815005-63816600	GM12878	blood:	n/a	chr2:63815660-63815669
23	RCOR1	chr2:63814999-63816670	GM12878	blood:	n/a	n/a
24	POLR2A	chr2:63815177-63816671	MCF-7	breast:	n/a	n/a
25	MAX	chr2:63815169-63816518	ECC-1	luminal epithelium:	n/a	n/a
26	GABPA	chr2:63815137-63816483	A549	lung:	n/a	n/a
27	TAF1	chr2:63815027-63816600	H1-hESC	embryonic stem cell:	n/a	n/a
28	SIN3AK20	chr2:63814862-63816586	H1-hESC	embryonic stem cell:	n/a	n/a
29	TAF1	chr2:63815206-63816446	HepG2	liver:	n/a	n/a
30	POLR2A	chr2:63815045-63817514	GM12891	blood:	n/a	n/a
31	POLR2A	chr2:63815149-63816629	HL-60	blood:	n/a	n/a
32	TCF7L2	chr2:63815145-63816421	HCT-116	colon:	n/a	n/a
33	MYC	chr2:63815185-63816841	K562	blood:	n/a	n/a
34	SMC3	chr2:63814833-63816633	Hela-S3	cervix:	n/a	n/a
35	MXI1	chr2:63814613-63817429	SK-N-SH	brain:	n/a	n/a
36	TEAD4	chr2:63815012-63815708	H1-hESC	embryonic stem cell:	n/a	n/a
37	POU2F2	chr2:63815125-63816452	GM12878	blood:	n/a	n/a
38	NFIC	chr2:63815190-63816390	GM12878	blood:	n/a	n/a
39	TEAD4	chr2:63815205-63816875	K562	blood:	n/a	n/a
40	YY1	chr2:63815135-63816449	HepG2	liver:	n/a	n/a
41	TAF1	chr2:63815118-63816781	A549	lung:	n/a	n/a
42	POLR2A	chr2:63815157-63816891	GM19099	blood:	n/a	n/a
43	POLR2A	chr2:63815161-63816639	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr2:63815139-63816554	GM18951	blood:	n/a	n/a
45	E2F4	chr2:63815165-63816355	K562	blood:	n/a	n/a
46	TCF12	chr2:63815032-63816614	A549	lung:	n/a	n/a
47	CHD2	chr2:63815164-63816471	H1-hESC	embryonic stem cell:	n/a	n/a
48	MXI1	chr2:63815153-63816813	GM12878	blood:	n/a	n/a
49	POLR2A	chr2:63815066-63817028	HL-60	blood:	n/a	n/a
50	TBP	chr2:63814979-63816981	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:63814867..63817469-chr2:63922056..63924960,2	MCF-7	breast:
2	chr2:63814652..63820726-chr2:63822860..63830564,18	K562	blood:
3	chr1:161014965..161015754-chr2:63815057..63815914,2	HCT-116	colon:
4	chr2:63814719..63818163-chr2:63820081..63823220,6	MCF-7	breast:
5	chr2:63814544..63817562-chr2:63819288..63824360,10	K562	blood:
6	chr2:63802150..63804372-chr2:63812471..63815243,3	K562	blood:

No data

Variant related genes	Relation type
MDH1	TF binding region
ENSG00000221085	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000014641	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10496102	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs12463603	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464471	0.81[GIH][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap]
rs12470478	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12472865	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12476015	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17618045	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17618390	1.00[YRI][hapmap]
rs17619012	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2054120	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2278718	0.85[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4671062	0.81[EUR][1000 genomes]
rs72806010	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72806027	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72806056	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72806058	0.80[EUR][1000 genomes]
rs72821631	0.83[EUR][1000 genomes]
rs72821632	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv1792289	chr2:63812148-63900292	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1109027	GNAO1	trans	lymphoblastoid	RTeQTL
rs1109027	POLR2E	trans	parietal	SCAN
rs1109027	CCT4	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63813000-63817800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr2:63813400-63817400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:63813400-63817400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr2:63813400-63817600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr2:63813600-63817000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr2:63813600-63817000	Active TSS	K562	blood
7	chr2:63813600-63817200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr2:63813800-63816800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:63813800-63817000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr2:63813800-63817000	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr2:63813800-63817200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr2:63814000-63817200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:63814000-63817400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr2:63814000-63817400	Active TSS	GM12878-XiMat	blood
15	chr2:63814200-63816800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:63814200-63817000	Active TSS	A549	lung
17	chr2:63814200-63817000	Active TSS	NHLF	lung
18	chr2:63814200-63820000	Active TSS	Right Ventricle	heart
19	chr2:63814400-63815400	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr2:63814400-63816800	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr2:63814400-63816800	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr2:63814400-63816800	Active TSS	Fetal Brain Male	brain
23	chr2:63814400-63817000	Active TSS	Brain Cingulate Gyrus	brain
24	chr2:63814400-63817000	Active TSS	HMEC	breast
25	chr2:63814400-63817000	Active TSS	NHDF-Ad	bronchial
26	chr2:63814400-63817400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:63814400-63819200	Active TSS	Right Atrium	heart
28	chr2:63814600-63815400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr2:63814600-63815400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:63814600-63815600	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr2:63814600-63816800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:63814600-63816800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:63814600-63816800	Active TSS	Muscle Satellite Cultured Cells	--
34	chr2:63814600-63816800	Active TSS	Fetal Intestine Small	intestine
35	chr2:63814600-63817000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:63814600-63817000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:63814600-63817000	Active TSS	Colon Smooth Muscle	Colon
38	chr2:63814600-63817200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:63814600-63817200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:63814600-63817200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:63814600-63817200	Active TSS	HSMM	muscle
42	chr2:63814600-63817600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr2:63814800-63815400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr2:63814800-63815400	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr2:63814800-63815400	Flanking Active TSS	Liver	Liver
46	chr2:63814800-63816600	Active TSS	Small Intestine	intestine
47	chr2:63814800-63816600	Active TSS	Stomach Smooth Muscle	stomach
48	chr2:63814800-63816800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:63814800-63816800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:63814800-63816800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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