Variant report

Variant	rs12476197
Chromosome Location	chr2:234601224-234601225
allele	C/G
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:10)
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	chr2:234601005-234601290	MCF-7	breast:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234356284..234357802-chr2:234598772..234601558,2	MCF-7	breast:
2	chr2:234599124..234606471-chr2:234613478..234621007,17	MCF-7	breast:
3	chr2:234473282..234477495-chr2:234598048..234603332,9	MCF-7	breast:
4	chr2:234388753..234400184-chr2:234596527..234603213,35	MCF-7	breast:
5	chr2:234600369..234602177-chr2:234775436..234777156,2	MCF-7	breast:
6	chr2:234393680..234401613-chr2:234597738..234605139,18	MCF-7	breast:
7	chr2:234472037..234477650-chr2:234599067..234602356,8	MCF-7	breast:
8	chr2:234597435..234606028-chr2:234613419..234620116,22	MCF-7	breast:
9	chr2:234387197..234390730-chr2:234600088..234603557,3	MCF-7	breast:
10	chr15:50714595..50716933-chr2:234599004..234601578,2	MCF-7	breast:

No data

Variant related genes	Relation type
UGT1A6	TF binding region
ENSG00000224814	Chromatin interaction
ENSG00000085982	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000224287	Chromatin interaction
ENSG00000077044	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1018124	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs10929293	0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs12052787	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs12053462	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12463641	0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs12463910	0.81[ASN][1000 genomes]
rs12466747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12466779	0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs12466997	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs12468274	0.81[ASN][1000 genomes]
rs12468356	0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs12468543	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs12472689	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12474215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12474980	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12475068	0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs12475934	0.81[ASN][1000 genomes]
rs12477216	0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs12479045	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs12479208	0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs1604144	0.81[GIH][hapmap];0.87[JPT][hapmap]
rs17862856	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17862857	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17862867	0.82[ASN][1000 genomes]
rs17862870	0.91[CHB][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs17862871	0.82[ASN][1000 genomes]
rs17862878	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs17863773	0.84[LWK][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs17863790	0.82[ASN][1000 genomes]
rs17863791	0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs17863792	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap]
rs17863798	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs17864684	0.81[AMR][1000 genomes]
rs17864686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17864696	0.82[ASN][1000 genomes]
rs17864705	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs17868325	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17868333	0.82[ASN][1000 genomes]
rs17868334	0.91[CHB][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs17868335	0.82[ASN][1000 genomes]
rs17868342	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs17874943	0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2003569	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs2011219	0.81[ASN][1000 genomes]
rs2013018	0.91[CHB][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs2013021	0.91[CHB][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs2013030	0.91[CHB][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs2602381	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2885295	0.91[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs28898595	0.82[ASN][1000 genomes]
rs28898596	0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs28898605	0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs28898615	0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs28898621	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs28899186	0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs28899187	0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs28899189	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs28946877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732218	0.91[CHB][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs3732219	0.82[ASN][1000 genomes]
rs3732220	0.91[CHB][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs3732221	0.91[CHB][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs3755320	0.82[ASN][1000 genomes]
rs3755321	0.91[CHB][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs3755322	0.82[ASN][1000 genomes]
rs3755323	0.82[ASN][1000 genomes]
rs3771342	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs3796088	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs3806591	0.91[CHB][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs3806593	0.91[CHB][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs3806594	0.91[CHB][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs3806595	0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs3892170	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs3893334	0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4233633	0.80[JPT][hapmap]
rs4485562	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4556969	0.91[CHB][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs4663325	0.80[JPT][hapmap]
rs4663326	0.91[CHB][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs4663327	0.80[JPT][hapmap]
rs4663871	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4663877	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4663945	0.91[CHB][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs4663964	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs4663968	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs5020121	0.82[ASN][1000 genomes]
rs6731242	0.84[TSI][hapmap]
rs6751673	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs6753317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7420193	0.91[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs904855	0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs904856	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][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	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv876016	chr2:234590527-234601669	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12476197	USP40	Cis_1M	lymphoblastoid	RTeQTL
rs12476197	SH3BP4	cis	cerebellum	SCAN
rs12476197	SPP2	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234597800-234608600	Weak transcription	Gastric	stomach
2	chr2:234599400-234608000	Weak transcription	HUVEC	blood vessel
3	chr2:234600200-234601400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:234600200-234601600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:234600200-234602600	Enhancers	A549	lung
6	chr2:234600400-234601600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:234600400-234601800	Enhancers	Colonic Mucosa	Colon
8	chr2:234600400-234608200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:234600600-234601400	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr2:234600600-234602000	Flanking Active TSS	NHEK	skin
11	chr2:234600800-234601400	Enhancers	Fetal Intestine Large	intestine
12	chr2:234600800-234601400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr2:234600800-234601400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr2:234600800-234601600	Enhancers	HMEC	breast
15	chr2:234600800-234602400	Enhancers	Fetal Kidney	kidney
16	chr2:234600800-234603000	Weak transcription	Right Atrium	heart
17	chr2:234601000-234601400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:234601000-234601400	Flanking Active TSS	Stomach Mucosa	stomach
19	chr2:234601000-234601800	Enhancers	Fetal Intestine Small	intestine
20	chr2:234601000-234602400	Weak transcription	Hela-S3	cervix
21	chr2:234601200-234601400	Flanking Active TSS	Liver	Liver
22	chr2:234601200-234602000	Weak transcription	Esophagus	oesophagus
23	chr2:234601200-234602200	Enhancers	Pancreas	Pancrea

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