Variant report

Variant	rs12429348
Chromosome Location	chr13:48611276-48611277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:55)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:55 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr13:48611217-48612718	GM18951	blood:	n/a	n/a
2	SP1	chr13:48611202-48612408	H1-hESC	embryonic stem cell:	n/a	chr13:48611787-48611798
3	POLR2A	chr13:48611092-48612781	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr13:48611178-48612552	MCF10A-Er-Src	breast:	n/a	n/a
5	MXI1	chr13:48611128-48612826	IMR90	lung:	n/a	n/a
6	POLR2A	chr13:48610965-48612561	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr13:48611264-48612740	GM12892	blood:	n/a	n/a
8	MYC	chr13:48611223-48612503	H1-hESC	embryonic stem cell:	n/a	n/a
9	TBP	chr13:48611183-48612513	H1-hESC	embryonic stem cell:	n/a	n/a
10	MXI1	chr13:48610981-48613175	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr13:48611028-48612883	Hela-S3	cervix:	n/a	n/a
12	MTA3	chr13:48611185-48612834	GM12878	blood:	n/a	n/a
13	MAX	chr13:48611057-48612451	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr13:48611209-48612458	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr13:48611250-48612532	HUVEC	blood vessel:	n/a	n/a
16	RELA	chr13:48611149-48612478	GM19099	blood:	n/a	n/a
17	POLR2A	chr13:48611141-48613548	SK-N-MC	brain:	n/a	n/a
18	SIN3AK20	chr13:48611227-48612596	MCF-7	breast:	n/a	n/a
19	POLR2A	chr13:48611268-48612564	GM12892	blood:	n/a	n/a
20	RCOR1	chr13:48611225-48612584	IMR90	lung:	n/a	n/a
21	E2F6	chr13:48611217-48612531	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr13:48611263-48613590	GM12891	blood:	n/a	n/a
23	POLR2A	chr13:48611253-48613185	Raji	blood:	n/a	n/a
24	POLR2A	chr13:48611238-48612605	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr13:48611173-48612550	PFSK-1	brain:	n/a	n/a
26	MAX	chr13:48611276-48612448	SK-N-SH	brain:	n/a	n/a
27	MXI1	chr13:48611222-48612420	HepG2	liver:	n/a	n/a
28	MAX	chr13:48611256-48612559	H1-hESC	embryonic stem cell:	n/a	n/a
29	CHD1	chr13:48611153-48611679	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAFK	chr13:48611167-48612321	HepG2	liver:	n/a	n/a
31	POLR2A	chr13:48611194-48613506	GM12878	blood:	n/a	n/a
32	POLR2A	chr13:48611252-48612447	HepG2	liver:	n/a	n/a
33	MAX	chr13:48611147-48612503	NB4	blood:	n/a	n/a
34	POLR2A	chr13:48611261-48613291	HepG2	liver:	n/a	n/a
35	TBP	chr13:48611183-48612439	Hela-S3	cervix:	n/a	n/a
36	CREB1	chr13:48611255-48612502	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr13:48611174-48612488	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr13:48611190-48612693	HepG2	liver:	n/a	n/a
39	CTCF	chr13:48611206-48612668	A549	lung:	n/a	chr13:48612207-48612220 chr13:48612269-48612278 chr13:48612205-48612221 chr13:48612204-48612222
40	MAX	chr13:48611266-48612439	Hela-S3	cervix:	n/a	n/a
41	HCFC1	chr13:48611144-48612577	Hela-S3	cervix:	n/a	n/a
42	TCF12	chr13:48611202-48612673	A549	lung:	n/a	chr13:48611299-48611308
43	MAX	chr13:48611214-48612578	A549	lung:	n/a	n/a
44	POLR2A	chr13:48611243-48613310	IMR90	lung:	n/a	n/a
45	POLR2A	chr13:48611263-48612517	SK-N-MC	brain:	n/a	n/a
46	MYC	chr13:48611259-48612485	NB4	blood:	n/a	n/a
47	FOXM1	chr13:48611275-48612591	ECC-1	luminal epithelium:	n/a	n/a
48	KAP1	chr13:48611179-48612496	HEK293	kidney:	n/a	n/a
49	POLR2A	chr13:48611236-48612491	Hela-S3	cervix:	n/a	n/a
50	E2F4	chr13:48610361-48612456	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:48573666..48577274-chr13:48610467..48613685,4	MCF-7	breast:
2	chr13:48610643..48613395-chr13:48668732..48670612,2	MCF-7	breast:
3	chr13:48611090..48611973-chr14:100704137..100705031,2	Hela-S3	cervix:
4	chr13:30424219..30424825-chr13:48611138..48612130,2	NB4	blood:

No data

Variant related genes	Relation type
NUDT15	TF binding region
ENSG00000136146	Chromatin interaction
ENSG00000227848	Chromatin interaction
ENSG00000136143	Chromatin interaction
ENSG00000258982	Chromatin interaction
ENSG00000100811	Chromatin interaction
ENSG00000122042	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11838539	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12427516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12427964	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12428055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12428102	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12429099	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429105	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12429746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429993	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12430076	0.85[AMR][1000 genomes]
rs12430172	0.85[AMR][1000 genomes]
rs12431057	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12431130	0.82[EUR][1000 genomes]
rs1968029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2182374	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2182375	0.80[MKK][hapmap];0.82[ASN][1000 genomes]
rs2182377	0.82[ASN][1000 genomes]
rs2897496	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35710390	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57698455	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57957392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58316588	0.82[EUR][1000 genomes]
rs58634823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61585711	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329615	1.00[JPT][hapmap]
rs8002322	0.82[ASN][1000 genomes]
rs840430	0.82[ASN][1000 genomes]
rs9534910	0.82[ASN][1000 genomes]
rs9534936	0.93[ASN][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	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS 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	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48576000-48611400	Weak transcription	Left Ventricle	heart
2	chr13:48602800-48611400	Weak transcription	Aorta	Aorta
3	chr13:48603800-48611400	Weak transcription	Ovary	ovary
4	chr13:48606600-48611400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr13:48607000-48611400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:48607000-48611400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:48610400-48611600	Flanking Active TSS	Dnd41	blood
8	chr13:48610400-48612800	Active TSS	K562	blood
9	chr13:48610400-48613000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr13:48610400-48613200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr13:48610600-48611600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr13:48610600-48611600	Flanking Active TSS	GM12878-XiMat	blood
13	chr13:48610800-48611400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr13:48610800-48611400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr13:48610800-48611400	Flanking Active TSS	HMEC	breast
16	chr13:48610800-48611600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr13:48610800-48611600	Flanking Active TSS	Fetal Lung	lung
18	chr13:48610800-48611600	Flanking Active TSS	NHEK	skin
19	chr13:48610800-48611800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr13:48610800-48612400	Active TSS	H1 Cell Line	embryonic stem cell
21	chr13:48610800-48612800	Active TSS	H9 Cell Line	embryonic stem cell
22	chr13:48610800-48613000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:48610800-48613000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr13:48610800-48613200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr13:48611000-48611400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr13:48611000-48611400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr13:48611000-48611400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr13:48611000-48611400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr13:48611000-48611400	Enhancers	Colonic Mucosa	Colon
30	chr13:48611000-48611400	Enhancers	Placenta	Placenta
31	chr13:48611000-48611400	Enhancers	Lung	lung
32	chr13:48611000-48611400	Enhancers	Pancreas	Pancrea
33	chr13:48611000-48611400	Enhancers	Stomach Mucosa	stomach
34	chr13:48611000-48611400	Flanking Active TSS	Hela-S3	cervix
35	chr13:48611000-48611600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr13:48611000-48611600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr13:48611000-48611600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr13:48611000-48611600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr13:48611000-48611600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr13:48611000-48611600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr13:48611000-48611600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr13:48611000-48611600	Flanking Active TSS	Fetal Kidney	kidney
43	chr13:48611000-48611600	Flanking Active TSS	Thymus	Thymus
44	chr13:48611000-48611600	Flanking Active TSS	HSMM	muscle
45	chr13:48611000-48611600	Flanking Active TSS	NHLF	lung
46	chr13:48611000-48611800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr13:48611000-48611800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr13:48611000-48611800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr13:48611000-48611800	Flanking Active TSS	HUVEC	blood vessel
50	chr13:48611000-48612600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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