Variant report

Variant	rs73534
Chromosome Location	chr12:30950209-30950210
allele	G/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	CEBPB	chr12:30949880-30950249	Hela-S3	cervix:	n/a	n/a
2	MAX	chr12:30949990-30950334	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr12:30947455-30950217	HUVEC	blood vessel:	n/a	n/a
4	ZNF384	chr12:30950103-30950318	K562	blood:	n/a	n/a
5	POLR2A	chr12:30949712-30950360	HUVEC	blood vessel:	n/a	n/a
6	TAF1	chr12:30949848-30950209	Hela-S3	cervix:	n/a	n/a
7	MAX	chr12:30947459-30950381	A549	lung:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
8	MAX	chr12:30949991-30950364	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr12:30949834-30950322	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr12:30949704-30950261	HCT-116	colon:	n/a	n/a
11	ZNF263	chr12:30948167-30950323	HEK293-T-REx	kidney:	n/a	chr12:30949957-30949966
12	POLR2A	chr12:30949721-30950275	U87	brain:	n/a	n/a
13	GATA3	chr12:30949840-30950361	MCF-7	breast:	n/a	n/a
14	POLR2A	chr12:30947330-30950355	Hela-S3	cervix:	n/a	n/a
15	TBP	chr12:30947584-30950261	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:30947377-30950489	U87	brain:	n/a	n/a
17	POLR2A	chr12:30947604-30950324	IMR90	lung:	n/a	n/a
18	E2F6	chr12:30949835-30950385	H1-hESC	embryonic stem cell:	n/a	n/a
19	MYC	chr12:30950142-30950311	MCF10A-Er-Src	breast:	n/a	n/a
20	MAX	chr12:30947501-30950261	Hela-S3	cervix:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
21	CHD2	chr12:30947585-30950215	Hela-S3	cervix:	n/a	chr12:30949618-30949628 chr12:30949531-30949541
22	GATA3	chr12:30947633-30950364	SK-N-SH	brain:	n/a	chr12:30949444-30949451 chr12:30948045-30948052 chr12:30948040-30948056
23	POLR2A	chr12:30949721-30950315	U87	brain:	n/a	n/a
24	POLR2A	chr12:30947452-30950270	Hela-S3	cervix:	n/a	n/a
25	RFX5	chr12:30949963-30950238	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr12:30947532-30950256	Hela-S3	cervix:	n/a	n/a
27	SIN3A	chr12:30949947-30950291	H1-hESC	embryonic stem cell:	n/a	n/a
28	RCOR1	chr12:30949858-30950298	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr12:30947383-30950297	U87	brain:	n/a	n/a
30	POLR2A	chr12:30947440-30950234	Hela-S3	cervix:	n/a	n/a
31	ZNF143	chr12:30949811-30950282	H1-hESC	embryonic stem cell:	n/a	n/a
32	JUN	chr12:30949919-30950209	K562	blood:	n/a	n/a
33	SMARCB1	chr12:30947494-30950210	Hela-S3	cervix:	n/a	chr12:30948297-30948306
34	MAFK	chr12:30949942-30950298	Hela-S3	cervix:	n/a	n/a
35	MAX	chr12:30947618-30950395	HCT-116	colon:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
36	TCF12	chr12:30947596-30950387	SK-N-SH	brain:	n/a	chr12:30948696-30948706
37	GATA3	chr12:30949895-30950246	T-47D	breast:	n/a	n/a
38	MAZ	chr12:30947796-30950214	Hela-S3	cervix:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
39	POLR2A	chr12:30947667-30950304	SK-N-SH	brain:	n/a	n/a
40	SMC3	chr12:30947497-30950255	Hela-S3	cervix:	n/a	chr12:30950004-30950012
41	MAX	chr12:30949731-30950335	SK-N-SH	brain:	n/a	n/a
42	GATA2	chr12:30949722-30950310	HUVEC	blood vessel:	n/a	n/a
43	MAX	chr12:30949879-30950375	H1-hESC	embryonic stem cell:	n/a	n/a
44	GTF2F1	chr12:30947586-30950250	Hela-S3	cervix:	n/a	n/a
45	MYC	chr12:30949889-30950366	MCF10A-Er-Src	breast:	n/a	n/a
46	USF2	chr12:30949949-30950272	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr12:30947501-30950305	MCF10A-Er-Src	breast:	n/a	n/a
48	RCOR1	chr12:30949942-30950265	K562	blood:	n/a	n/a
49	POLR2A	chr12:30949734-30950329	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr12:30947489-30950302	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:30906304..30909589-chr12:30948532..30951386,3	K562	blood:
2	chr12:30949301..30951122-chr12:30954767..30957062,2	MCF-7	breast:
3	chr12:30949445..30950276-chr9:2015332..2016130,2	Hela-S3	cervix:
4	chr12:30949838..30951631-chr12:30954389..30956016,2	K562	blood:

Variant related genes	Relation type
LINC00941	TF binding region
ENSG00000246331	Chromatin interaction
ENSG00000080503	Chromatin interaction
ENSG00000110888	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs166276	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs166277	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs171760	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs187673	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2352525	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs256655	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs256663	0.96[ASN][1000 genomes]
rs256665	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256666	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256667	0.96[ASN][1000 genomes]
rs256669	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256670	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs256671	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256672	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256673	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256674	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256675	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256676	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256677	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256679	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256680	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256681	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256682	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256683	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256684	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256685	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256687	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs256689	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256690	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256692	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256693	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256694	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256695	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256696	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs256697	0.96[ASN][1000 genomes]
rs256698	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs256699	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs538731	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv34091	chr12:30927650-31061815	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30948000-30950400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr12:30948200-30950400	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr12:30948200-30950400	Active TSS	Brain Anterior Caudate	brain
4	chr12:30948400-30950400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr12:30948400-30950400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr12:30948600-30950400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:30948600-30950400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:30948600-30950400	Active TSS	A549	lung
9	chr12:30948600-30950400	Active TSS	Osteobl	bone
10	chr12:30948800-30950400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:30948800-30950400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr12:30948800-30950400	Active TSS	HSMM	muscle
13	chr12:30949000-30950400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
14	chr12:30949000-30950400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr12:30949200-30950400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:30949400-30950400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:30949400-30950400	Active TSS	HMEC	breast
18	chr12:30949600-30950400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:30949600-30950400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
20	chr12:30949600-30952200	Weak transcription	HepG2	liver
21	chr12:30949800-30950400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:30949800-30950400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:30949800-30950400	Flanking Active TSS	HUVEC	blood vessel
24	chr12:30949800-30950400	Flanking Active TSS	NHEK	skin
25	chr12:30950000-30950400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
26	chr12:30950000-30950400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:30950000-30950400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr12:30950000-30950400	Bivalent Enhancer	Placenta	Placenta
29	chr12:30950000-30950400	Enhancers	Right Atrium	heart
30	chr12:30950000-30950400	Flanking Active TSS	NH-A	brain
31	chr12:30950000-30950800	Flanking Active TSS	Hela-S3	cervix
32	chr12:30950200-30950400	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:30950200-30950400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
34	chr12:30950200-30950400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr12:30950200-30950400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:30950200-30950400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:30950200-30950400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:30950200-30950400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:30950200-30950400	Bivalent Enhancer	Adipose Nuclei	Adipose
40	chr12:30950200-30950400	Enhancers	Liver	Liver
41	chr12:30950200-30950400	Bivalent Enhancer	Brain Germinal Matrix	brain
42	chr12:30950200-30950400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:30950200-30950400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr12:30950200-30950400	Bivalent Enhancer	Fetal Muscle Leg	muscle
45	chr12:30950200-30950400	Bivalent Enhancer	Fetal Stomach	stomach
46	chr12:30950200-30950400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
47	chr12:30950200-30950400	Active TSS	Right Ventricle	heart
48	chr12:30950200-30950400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
49	chr12:30950200-30950400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
50	chr12:30950200-30950400	Active TSS	NHDF-Ad	bronchial

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