Variant report

Variant	rs10747562
Chromosome Location	chr12:49505184-49505185
allele	C/T
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	NFYA	chr12:49504374-49505294	Hela-S3	cervix:	n/a	chr12:49504714-49504724 chr12:49504711-49504726
2	HCFC1	chr12:49502367-49505574	Hela-S3	cervix:	n/a	n/a
3	WRNIP1	chr12:49504731-49505339	GM12878	blood:	n/a	n/a
4	MAZ	chr12:49502507-49505354	IMR90	lung:	n/a	chr12:49504015-49504025 chr12:49503402-49503411
5	RCOR1	chr12:49505023-49505323	HepG2	liver:	n/a	n/a
6	MAX	chr12:49504068-49505428	A549	lung:	n/a	n/a
7	SIN3A	chr12:49503765-49505270	H1-hESC	embryonic stem cell:	n/a	chr12:49504157-49504170
8	RCOR1	chr12:49504444-49505245	K562	blood:	n/a	n/a
9	SP1	chr12:49504023-49505260	HCT-116	colon:	n/a	chr12:49504775-49504789 chr12:49504027-49504036 chr12:49504025-49504037 chr12:49504025-49504037 chr12:49504513-49504520 chr12:49504026-49504035 chr12:49504501-49504513 chr12:49505023-49505032 chr12:49504502-49504511 chr12:49504611-49504624 chr12:49504501-49504513
10	SMARCC1	chr12:49504222-49505278	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:49503785-49505341	K562	blood:	n/a	n/a
12	SMARCC2	chr12:49504298-49505215	Hela-S3	cervix:	n/a	n/a
13	MAX	chr12:49504192-49505193	NB4	blood:	n/a	n/a
14	ZKSCAN1	chr12:49504268-49505296	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr12:49504286-49505378	A549	lung:	n/a	chr12:49505091-49505098
16	CBX3	chr12:49504151-49505504	K562	blood:	n/a	n/a
17	NFYB	chr12:49504435-49505193	GM12878	blood:	n/a	chr12:49504714-49504724 chr12:49504713-49504728 chr12:49504711-49504726
18	MXI1	chr12:49502736-49505505	SK-N-SH	brain:	n/a	n/a
19	REST	chr12:49503164-49505359	H1-neurons	neurons:	n/a	chr12:49504157-49504170 chr12:49504546-49504555
20	RCOR1	chr12:49504194-49505266	K562	blood:	n/a	n/a
21	MAZ	chr12:49503635-49505225	K562	blood:	n/a	chr12:49504015-49504025
22	GATA2	chr12:49504026-49505319	SH-SY5Y	brain:	n/a	chr12:49504833-49504840 chr12:49504826-49504847 chr12:49504833-49504840 chr12:49504833-49504840 chr12:49504829-49504840
23	GATA1	chr12:49504116-49505379	PBDE	blood:	n/a	chr12:49504833-49504840 chr12:49504826-49504847 chr12:49504833-49504840 chr12:49504833-49504840 chr12:49504829-49504840
24	POLR2A	chr12:49504026-49505362	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49499760..49506124-chr12:49657415..49661017,8	K562	blood:
2	chr12:49501897..49506471-chr12:49657604..49660787,6	MCF-7	breast:
3	chr12:49497954..49506685-chr12:49522695..49526444,13	MCF-7	breast:
4	chr12:49500412..49506796-chr12:49520694..49526646,13	MCF-7	breast:
5	chr12:49481573..49488751-chr12:49501255..49506032,14	K562	blood:
6	chr12:49452282..49457106-chr12:49501761..49505806,6	K562	blood:
7	chr12:49454631..49456849-chr12:49504734..49506537,2	K562	blood:
8	chr12:49497683..49501522-chr12:49502793..49506157,6	MCF-7	breast:
9	chr12:49448339..49452151-chr12:49502290..49505835,5	K562	blood:
10	chr12:49493937..49507579-chr12:49519161..49528577,46	K562	blood:
11	chr12:49484670..49486982-chr12:49502782..49505716,3	MCF-7	breast:
12	chr12:49462517..49467862-chr12:49502773..49505660,4	MCF-7	breast:
13	chr12:49494625..49497583-chr12:49503170..49505845,3	MCF-7	breast:

Variant related genes	Relation type
LMBR1L	TF binding region
ENSG00000257346	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000167550	Chromatin interaction
ENSG00000139549	Chromatin interaction
ENSG00000123416	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1039225	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap]
rs1057548	0.80[EUR][1000 genomes]
rs10747561	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10747563	0.94[CHB][hapmap]
rs10783302	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783304	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783306	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10783307	0.92[CEU][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10783308	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875922	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10875924	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875927	0.80[EUR][1000 genomes]
rs10875928	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap]
rs10875931	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.91[YRI][hapmap]
rs10875934	0.94[CHB][hapmap]
rs11168857	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs11168862	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168867	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11168874	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168882	0.81[EUR][1000 genomes]
rs11168884	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs11168885	0.80[EUR][1000 genomes]
rs11168890	0.82[EUR][1000 genomes]
rs11168893	0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap]
rs11168894	0.82[EUR][1000 genomes]
rs11168910	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap]
rs11837207	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12227296	0.82[ASN][1000 genomes]
rs12228775	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12229524	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs12306494	0.83[ASN][1000 genomes]
rs12318740	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1476137	0.96[CEU][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1476138	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1874908	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap]
rs1991427	0.88[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs2047101	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2114846	0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs2162644	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs2241727	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279596	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2334930	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap]
rs2753	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3741621	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57853986	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7306084	0.94[CHB][hapmap]
rs73110168	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs731350	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7954521	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs7954530	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap]
rs7957983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7957998	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap]
rs7958241	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7958572	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7959497	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs7969963	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7969967	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7976890	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7978448	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7978659	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9325145	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9788139	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9788140	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10747562	POU6F1	cis	parietal	SCAN
rs10747562	C19orf55	trans	cerebellum	SCAN
rs10747562	DDN	cis	Muscle Skeletal	GTEx
rs10747562	TFCP2	cis	parietal	SCAN
rs10747562	CCDC65	cis	Artery Aorta	GTEx
rs10747562	RHEBL1	cis	parietal	SCAN
rs10747562	RP11-386G11.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49503000-49505200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:49503200-49505200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr12:49503200-49505200	Active TSS	Right Atrium	heart
4	chr12:49503200-49505400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr12:49503400-49505200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:49503400-49505200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:49503400-49505200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:49503400-49505200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:49503400-49505200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr12:49503400-49505200	Active TSS	HSMMtube	muscle
11	chr12:49503400-49505400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr12:49503400-49505400	Active TSS	Rectal Smooth Muscle	rectum
13	chr12:49503400-49505400	Active TSS	NHLF	lung
14	chr12:49503600-49505200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr12:49503600-49505200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:49503600-49505200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:49503600-49505200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:49503600-49505200	Active TSS	Brain Angular Gyrus	brain
19	chr12:49503600-49505200	Active TSS	Brain Anterior Caudate	brain
20	chr12:49503600-49505200	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr12:49503600-49505200	Active TSS	Colon Smooth Muscle	Colon
22	chr12:49503600-49505200	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr12:49503600-49505200	Active TSS	Psoas Muscle	Psoas
24	chr12:49503600-49505200	Active TSS	NH-A	brain
25	chr12:49503600-49505400	Active TSS	H1 Cell Line	embryonic stem cell
26	chr12:49503600-49505400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:49503600-49505400	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr12:49503600-49505400	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr12:49503600-49505400	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr12:49503600-49505400	Active TSS	Brain Cingulate Gyrus	brain
31	chr12:49503600-49505400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:49503600-49505400	Active TSS	Colonic Mucosa	Colon
33	chr12:49503600-49505400	Active TSS	Fetal Brain Female	brain
34	chr12:49503600-49505400	Active TSS	Thymus	Thymus
35	chr12:49503600-49505400	Active TSS	A549	lung
36	chr12:49503600-49505400	Bivalent/Poised TSS	HepG2	liver
37	chr12:49503800-49505200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:49503800-49505200	Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr12:49503800-49505200	Active TSS	Brain Hippocampus Middle	brain
40	chr12:49503800-49505200	Active TSS	Brain Substantia Nigra	brain
41	chr12:49503800-49505200	Active TSS	Fetal Stomach	stomach
42	chr12:49504000-49505200	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr12:49504600-49505200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:49504600-49505400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:49504800-49505200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:49504800-49505200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:49504800-49505200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr12:49504800-49505200	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr12:49504800-49505200	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr12:49504800-49505200	Flanking Active TSS	Primary T cells fromperipheralblood	blood

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