Variant report

Variant	rs12228013
Chromosome Location	chr12:39837815-39837816
allele	A/G
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	MAZ	chr12:39835741-39837909	K562	blood:	n/a	n/a
2	GATA2	chr12:39836783-39838597	SH-SY5Y	brain:	n/a	n/a
3	HNF4G	chr12:39837232-39837822	HepG2	liver:	n/a	chr12:39837527-39837539 chr12:39837526-39837540 chr12:39837526-39837539 chr12:39837533-39837540 chr12:39837525-39837540 chr12:39837526-39837540 chr12:39837527-39837540 chr12:39837527-39837539 chr12:39837527-39837539 chr12:39837525-39837540 chr12:39837524-39837542 chr12:39837526-39837540 chr12:39837525-39837540 chr12:39837527-39837540 chr12:39837526-39837534 chr12:39837527-39837539 chr12:39837527-39837540 chr12:39837525-39837540
4	MAX	chr12:39836853-39838085	NB4	blood:	n/a	n/a
5	POLR2A	chr12:39835866-39838030	H1-neurons	neurons:	n/a	n/a
6	SP1	chr12:39836689-39837910	A549	lung:	n/a	chr12:39837111-39837125 chr12:39837021-39837030 chr12:39837305-39837319 chr12:39837022-39837031 chr12:39837566-39837580 chr12:39837022-39837031 chr12:39837227-39837238
7	CREB1	chr12:39836233-39837853	HepG2	liver:	n/a	n/a
8	MTA3	chr12:39836735-39837903	GM12878	blood:	n/a	n/a
9	SMC3	chr12:39837463-39837858	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:39836664-39838074	HepG2	liver:	n/a	n/a
11	HEY1	chr12:39836668-39837841	HepG2	liver:	n/a	chr12:39836939-39836954 chr12:39837446-39837461 chr12:39837084-39837099
12	FOXA1	chr12:39837262-39838107	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:39835827-39837964	Hela-S3	cervix:	n/a	n/a
14	MXI1	chr12:39835267-39838054	Hela-S3	cervix:	n/a	n/a
15	MAX	chr12:39835821-39838126	A549	lung:	n/a	n/a
16	HEY1	chr12:39836686-39837824	HepG2	liver:	n/a	chr12:39836939-39836954 chr12:39837446-39837461 chr12:39837084-39837099
17	SMARCB1	chr12:39835989-39837833	Hela-S3	cervix:	n/a	n/a
18	HNF4A	chr12:39836606-39837958	HepG2	liver:	n/a	chr12:39837527-39837539 chr12:39837526-39837540 chr12:39837526-39837539 chr12:39837533-39837540 chr12:39837525-39837540 chr12:39837525-39837540 chr12:39837526-39837540 chr12:39837527-39837540 chr12:39837527-39837539 chr12:39837527-39837539 chr12:39837525-39837540 chr12:39837524-39837542 chr12:39837027-39837041 chr12:39837526-39837540 chr12:39837525-39837540 chr12:39837527-39837540 chr12:39837526-39837534 chr12:39837527-39837539 chr12:39837527-39837540 chr12:39837525-39837540
19	REST	chr12:39836068-39838099	A549	lung:	n/a	chr12:39836286-39836304 chr12:39836545-39836555 chr12:39837289-39837302
20	MYBL2	chr12:39836709-39838059	HepG2	liver:	n/a	n/a
21	TAF1	chr12:39835989-39838004	H1-neurons	neurons:	n/a	n/a
22	KAP1	chr12:39836891-39838149	HEK293	kidney:	n/a	n/a
23	RELA	chr12:39836853-39837843	GM18951	blood:	n/a	n/a
24	CTCF	chr12:39835556-39838407	A549	lung:	n/a	chr12:39836641-39836654 chr12:39837116-39837129 chr12:39837803-39837811
25	RAD21	chr12:39836949-39837955	HepG2	liver:	n/a	n/a
26	MAZ	chr12:39836834-39837819	HepG2	liver:	n/a	n/a
27	MYC	chr12:39837801-39838090	MCF10A-Er-Src	breast:	n/a	n/a
28	MAX	chr12:39835599-39838058	Hela-S3	cervix:	n/a	n/a
29	MYC	chr12:39836062-39838312	A549	lung:	n/a	n/a
30	GATA3	chr12:39836647-39837823	A549	lung:	n/a	n/a
31	CTCF	chr12:39836677-39837873	SK-N-SH	brain:	n/a	chr12:39837116-39837129 chr12:39837803-39837811
32	MXI1	chr12:39835698-39838095	HepG2	liver:	n/a	n/a
33	SP1	chr12:39836658-39837872	A549	lung:	n/a	chr12:39837111-39837125 chr12:39837021-39837030 chr12:39837305-39837319 chr12:39837022-39837031 chr12:39837566-39837580 chr12:39837022-39837031 chr12:39837227-39837238
34	POLR2A	chr12:39836680-39837822	HepG2	liver:	n/a	n/a
35	POLR2A	chr12:39836438-39837820	HepG2	liver:	n/a	n/a
36	TCF12	chr12:39836737-39837831	A549	lung:	n/a	n/a
37	MYC	chr12:39835645-39837825	K562	blood:	n/a	n/a
38	WRNIP1	chr12:39837414-39837849	GM12878	blood:	n/a	n/a
39	FOXA2	chr12:39836574-39837841	A549	lung:	n/a	n/a
40	MAX	chr12:39835939-39837816	HepG2	liver:	n/a	n/a
41	MAX	chr12:39836180-39838103	A549	lung:	n/a	n/a
42	POLR2A	chr12:39836284-39837963	HepG2	liver:	n/a	n/a
43	HA-E2F1	chr12:39835921-39837968	MCF-7	breast:	n/a	chr12:39836776-39836785 chr12:39836478-39836488 chr12:39836671-39836686 chr12:39837321-39837331
44	EP300	chr12:39836739-39837861	A549	lung:	n/a	n/a
45	MAX	chr12:39835969-39838037	A549	lung:	n/a	n/a
46	TFAP2C	chr12:39836230-39837837	Hela-S3	cervix:	n/a	chr12:39837335-39837350
47	POLR2A	chr12:39835661-39838101	H1-neurons	neurons:	n/a	n/a
48	MYBL2	chr12:39836705-39837922	HepG2	liver:	n/a	n/a
49	ARID3A	chr12:39836791-39838267	HepG2	liver:	n/a	n/a
50	ZNF263	chr12:39835862-39837920	HEK293-T-REx	kidney:	n/a	chr12:39836957-39836966 chr12:39837569-39837578

No.	Distal block	Cell Line	Cell type
1	chr12:39694207..39696152-chr12:39837237..39840087,2	K562	blood:
2	chr12:39757176..39762110-chr12:39835391..39838507,4	MCF-7	breast:
3	chr12:39837458..39839438-chr12:39863406..39864910,2	MCF-7	breast:
4	chr12:39759047..39762172-chr12:39834495..39838400,6	MCF-7	breast:
5	chr1:117602515..117604525-chr12:39835821..39838061,2	MCF-7	breast:
6	chr12:39723120..39728244-chr12:39834929..39837982,4	MCF-7	breast:
7	chr12:39836935..39837833-chr17:39844695..39845389,2	Hela-S3	cervix:

Variant related genes	Relation type
KIF21A	TF binding region
ENSG00000252974	TF binding region
ENSG00000139116	Chromatin interaction
ENSG00000116830	Chromatin interaction
ENSG00000173812	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10877173	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10877201	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs11172144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172162	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];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172366	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172616	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172645	0.95[EUR][1000 genomes]
rs11172647	0.95[EUR][1000 genomes]
rs11172687	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11172692	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172697	0.95[EUR][1000 genomes]
rs11172713	0.90[JPT][hapmap]
rs11172722	0.83[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs11172794	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11172848	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs11172896	0.81[EUR][1000 genomes]
rs11172897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12227286	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs12227668	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12228617	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12229160	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12229370	0.97[EUR][1000 genomes]
rs12230055	0.97[EUR][1000 genomes]
rs1512941	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs17126997	0.81[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs17127070	0.93[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs17127094	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs17127129	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17127138	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271478	1.00[JPT][hapmap]
rs2292491	0.93[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs35790935	0.97[EUR][1000 genomes]
rs35858791	0.97[EUR][1000 genomes]
rs4072006	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4285917	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4294600	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs4298947	0.91[EUR][1000 genomes]
rs4639970	0.97[EUR][1000 genomes]
rs57847223	0.95[EUR][1000 genomes]
rs58036566	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60263267	0.80[AFR][1000 genomes]
rs61258856	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581228	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7133376	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7133599	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7294474	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7302302	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7308138	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs73088816	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7309234	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes]
rs73094447	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73094449	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73094488	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7310178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7310871	0.95[EUR][1000 genomes]
rs7312611	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs73268359	0.81[EUR][1000 genomes]
rs74086536	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7966841	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs7970944	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7976275	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7980595	0.93[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]

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	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv3436594	chr12:39835210-39838058	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12228013	LRRK2	cis	parietal	SCAN
rs12228013	ABCD2	cis	multi-tissue	Pritchard

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39834000-39838000	Active TSS	Right Atrium	heart
2	chr12:39834200-39838000	Active TSS	Brain Angular Gyrus	brain
3	chr12:39835800-39838000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:39836000-39838000	Active TSS	Aorta	Aorta
5	chr12:39836800-39838000	Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr12:39837200-39838000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:39837200-39838000	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr12:39837400-39838000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
9	chr12:39837400-39838000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:39837400-39838000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr12:39837400-39838000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:39837400-39838000	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr12:39837400-39838000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr12:39837400-39838000	Flanking Active TSS	Fetal Brain Male	brain
15	chr12:39837400-39838000	Flanking Active TSS	Fetal Lung	lung
16	chr12:39837400-39838000	Flanking Active TSS	GM12878-XiMat	blood
17	chr12:39837400-39838000	Flanking Active TSS	Hela-S3	cervix
18	chr12:39837400-39838000	Flanking Active TSS	HMEC	breast
19	chr12:39837400-39838000	Flanking Active TSS	HUVEC	blood vessel
20	chr12:39837400-39838000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
21	chr12:39837400-39838200	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr12:39837400-39838200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr12:39837400-39838200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr12:39837400-39838200	Flanking Active TSS	Osteobl	bone
25	chr12:39837600-39838000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:39837600-39838000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:39837600-39838000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:39837600-39838000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
29	chr12:39837600-39838000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
30	chr12:39837600-39838000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
31	chr12:39837600-39838000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:39837600-39838000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:39837600-39838000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:39837600-39838000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
35	chr12:39837600-39838000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr12:39837600-39838000	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr12:39837600-39838000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr12:39837600-39838000	Flanking Active TSS	Fetal Intestine Small	intestine
39	chr12:39837600-39838000	Flanking Active TSS	Fetal Stomach	stomach
40	chr12:39837600-39838000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr12:39837600-39838000	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr12:39837600-39838000	Flanking Active TSS	HSMM	muscle
43	chr12:39837600-39838000	Flanking Active TSS	HSMMtube	muscle
44	chr12:39837600-39838000	Flanking Active TSS	NHLF	lung
45	chr12:39837600-39838200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr12:39837600-39838200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:39837600-39838200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:39837600-39838200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:39837600-39838200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr12:39837600-39838200	Flanking Active TSS	Liver	Liver

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