Variant report

Variant	rs12475932
Chromosome Location	chr2:209130292-209130293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:228)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:228 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:209130030-209130468	PFSK-1	brain:	n/a	n/a
2	MBD4	chr2:209129927-209131651	HepG2	liver:	n/a	n/a
3	CREB1	chr2:209130155-209131109	ECC-1	luminal epithelium:	n/a	n/a
4	CEBPB	chr2:209130216-209131085	HepG2	liver:	n/a	n/a
5	USF1	chr2:209130076-209131203	ECC-1	luminal epithelium:	n/a	n/a
6	TBL1XR1	chr2:209129765-209131669	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:209130039-209131427	K562	blood:	n/a	n/a
8	MAX	chr2:209130016-209131566	ECC-1	luminal epithelium:	n/a	chr2:209130353-209130362
9	MYC	chr2:209129863-209131263	K562	blood:	n/a	chr2:209130353-209130362
10	GATA1	chr2:209129668-209131288	K562	blood:	n/a	chr2:209130018-209130025 chr2:209130324-209130332
11	POLR2A	chr2:209129927-209131567	GM12892	blood:	n/a	n/a
12	POLR2A	chr2:209129919-209131492	GM12878	blood:	n/a	n/a
13	SP1	chr2:209129960-209131238	HCT-116	colon:	n/a	chr2:209130960-209130973 chr2:209130951-209130963
14	GTF2F1	chr2:209130249-209130481	H1-hESC	embryonic stem cell:	n/a	n/a
15	PAX5	chr2:209130108-209130407	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:209130091-209130445	GM12891	blood:	n/a	n/a
17	POLR2A	chr2:209129908-209131339	ProgFib	skin:	n/a	n/a
18	POLR2A	chr2:209129665-209132065	GM12891	blood:	n/a	n/a
19	POLR2A	chr2:209130046-209131501	GM15510	blood:	n/a	n/a
20	POLR2A	chr2:209130054-209131410	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:209130035-209131391	GM12891	blood:	n/a	n/a
22	ELK1	chr2:209130142-209131271	GM12878	blood:	n/a	n/a
23	REST	chr2:209130121-209131403	A549	lung:	n/a	chr2:209131202-209131220
24	CEBPB	chr2:209130033-209131096	GM12878	blood:	n/a	n/a
25	FOXM1	chr2:209130035-209131509	GM12878	blood:	n/a	n/a
26	POLR2A	chr2:209130056-209131196	K562	blood:	n/a	n/a
27	POLR2A	chr2:209130020-209130351	ECC-1	luminal epithelium:	n/a	n/a
28	MAFK	chr2:209129926-209131045	HepG2	liver:	n/a	n/a
29	MYBL2	chr2:209129979-209131322	HepG2	liver:	n/a	n/a
30	NFIC	chr2:209129999-209131096	HepG2	liver:	n/a	n/a
31	HEY1	chr2:209130080-209130358	K562	blood:	n/a	n/a
32	POLR2A	chr2:209130085-209131198	HCT-116	colon:	n/a	n/a
33	POLR2A	chr2:209129977-209130443	GM12891	blood:	n/a	n/a
34	MAZ	chr2:209130274-209131469	K562	blood:	n/a	chr2:209130353-209130362
35	SIX5	chr2:209130220-209131059	A549	lung:	n/a	n/a
36	POLR2A	chr2:209129750-209131632	GM12892	blood:	n/a	n/a
37	MAX	chr2:209129806-209131369	A549	lung:	n/a	chr2:209130353-209130362
38	FOS	chr2:209130135-209130976	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr2:209129719-209131530	GM19099	blood:	n/a	n/a
40	CBX3	chr2:209130148-209131131	K562	blood:	n/a	n/a
41	RCOR1	chr2:209130143-209131448	K562	blood:	n/a	n/a
42	POU2F2	chr2:209130134-209130368	GM12878	blood:	n/a	chr2:209130344-209130366 chr2:209130349-209130359 chr2:209130351-209130358
43	POLR2A	chr2:209129898-209131869	GM12878	blood:	n/a	n/a
44	USF2	chr2:209129894-209131003	HepG2	liver:	n/a	n/a
45	POLR2A	chr2:209130156-209131472	PFSK-1	brain:	n/a	n/a
46	POLR2A	chr2:209129957-209131634	GM12878	blood:	n/a	n/a
47	POLR2A	chr2:209130244-209130298	A549	lung:	n/a	n/a
48	TAF1	chr2:209130055-209130516	GM12878	blood:	n/a	n/a
49	FOSL2	chr2:209130251-209131121	A549	lung:	n/a	n/a
50	SIN3A	chr2:209130131-209131898	H1-hESC	embryonic stem cell:	n/a	chr2:209131049-209131062

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:208393863..208396191-chr2:209128319..209130637,2	K562	blood:
2	chr2:209123964..209126958-chr2:209128019..209130689,2	K562	blood:
3	chr2:209129671..209132812-chr2:209132994..209136144,5	MCF-7	breast:
4	chr2:209128359..209130743-chr2:209169171..209171063,2	K562	blood:
5	chr2:209116323..209122695-chr2:209127326..209132568,14	K562	blood:
6	chr2:209119923..209123053-chr2:209129009..209130826,3	MCF-7	breast:
7	chr2:209116323..209123332-chr2:209127326..209134005,17	K562	blood:
8	chr2:209129669..209131681-chr2:209132251..209135245,2	K562	blood:
9	chr2:209117138..209121626-chr2:209129108..209132782,7	MCF-7	breast:

No data

Variant related genes	Relation type
PIKFYVE	TF binding region
ENSG00000223725	Chromatin interaction
ENSG00000118260	Chromatin interaction
ENSG00000231908	Chromatin interaction
ENSG00000228380	Chromatin interaction
ENSG00000138413	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10173938	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10174541	0.94[EUR][1000 genomes]
rs10176626	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10177810	0.81[EUR][1000 genomes]
rs10186350	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs10189031	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10194539	0.94[EUR][1000 genomes]
rs10198535	0.96[EUR][1000 genomes]
rs10497897	0.94[EUR][1000 genomes]
rs10497898	0.94[EUR][1000 genomes]
rs10932260	0.96[EUR][1000 genomes]
rs11538998	1.00[CHD][hapmap]
rs11885913	1.00[CHD][hapmap]
rs11895188	0.89[CEU][hapmap];1.00[CHD][hapmap]
rs11898653	0.92[EUR][1000 genomes]
rs11901959	0.94[EUR][1000 genomes]
rs11902124	1.00[CHD][hapmap]
rs12185709	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694101	1.00[ASN][1000 genomes]
rs12694104	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392540	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13395304	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407268	0.81[EUR][1000 genomes]
rs13407897	0.94[EUR][1000 genomes]
rs13412043	0.94[EUR][1000 genomes]
rs1347664	1.00[CHD][hapmap]
rs1437413	1.00[CHD][hapmap]
rs1584200	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16841236	1.00[CHD][hapmap]
rs17700235	1.00[CHD][hapmap]
rs1816612	1.00[CHD][hapmap]
rs1866046	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs1900239	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2304545	0.83[EUR][1000 genomes]
rs2363465	0.99[EUR][1000 genomes]
rs2363466	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28418905	0.83[EUR][1000 genomes]
rs35293936	1.00[CHD][hapmap]
rs4462735	0.82[MEX][hapmap];0.82[TSI][hapmap]
rs4673391	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4673393	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4673394	0.90[CEU][hapmap]
rs4675748	0.81[CEU][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4675751	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs6435435	1.00[CHD][hapmap]
rs66887797	0.96[EUR][1000 genomes]
rs6724208	0.96[EUR][1000 genomes]
rs6725418	1.00[ASN][1000 genomes]
rs6736599	0.96[EUR][1000 genomes]
rs67669827	0.94[EUR][1000 genomes]
rs67965883	0.85[EUR][1000 genomes]
rs73056463	0.94[EUR][1000 genomes]
rs7355562	0.87[EUR][1000 genomes]
rs7557303	0.94[EUR][1000 genomes]
rs7565247	1.00[ASN][1000 genomes]
rs7583022	0.82[MEX][hapmap]
rs7587752	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7592472	0.81[EUR][1000 genomes]
rs9288392	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs999890	0.90[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs999891	0.90[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12475932	GPR1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209129600-209130400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr2:209129600-209130400	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr2:209129600-209130600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:209129600-209130600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:209129600-209130800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:209129600-209130800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:209129600-209132000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:209129800-209130400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:209129800-209130400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:209129800-209130400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:209129800-209130400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
12	chr2:209129800-209130400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr2:209129800-209130400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr2:209129800-209130400	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr2:209129800-209130400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr2:209129800-209130400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
17	chr2:209129800-209130400	Flanking Active TSS	Fetal Brain Female	brain
18	chr2:209129800-209130400	Flanking Active TSS	Fetal Heart	heart
19	chr2:209129800-209130400	Flanking Active TSS	Fetal Kidney	kidney
20	chr2:209129800-209130400	Flanking Active TSS	Fetal Lung	lung
21	chr2:209129800-209130400	Flanking Active TSS	Fetal Stomach	stomach
22	chr2:209129800-209130400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr2:209129800-209130400	Flanking Active TSS	GM12878-XiMat	blood
24	chr2:209129800-209130600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr2:209129800-209130600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:209129800-209130600	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr2:209129800-209130600	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr2:209129800-209130600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:209129800-209130600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr2:209129800-209130600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr2:209129800-209130600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr2:209129800-209130600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:209129800-209130600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr2:209129800-209130600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:209129800-209130600	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr2:209129800-209130600	Flanking Active TSS	Hela-S3	cervix
37	chr2:209129800-209130600	Flanking Active TSS	HMEC	breast
38	chr2:209129800-209130600	Flanking Active TSS	HSMM	muscle
39	chr2:209129800-209130600	Flanking Active TSS	HSMMtube	muscle
40	chr2:209129800-209130600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr2:209129800-209130600	Flanking Active TSS	NHEK	skin
42	chr2:209129800-209130600	Flanking Active TSS	Osteobl	bone
43	chr2:209129800-209130800	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr2:209129800-209130800	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr2:209129800-209130800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr2:209129800-209130800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr2:209129800-209130800	Flanking Active TSS	NHDF-Ad	bronchial
48	chr2:209129800-209131400	Active TSS	Colonic Mucosa	Colon
49	chr2:209129800-209131600	Active TSS	Esophagus	oesophagus
50	chr2:209129800-209132800	Active TSS	H1 Cell Line	embryonic stem cell

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