Variant report

Variant	rs256655
Chromosome Location	chr12:30949511-30949512
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	POLR2A	chr12:30949451-30949630	A549	lung:	n/a	n/a
2	MYC	chr12:30948756-30949648	H1-hESC	embryonic stem cell:	n/a	chr12:30949347-30949356
3	NRF1	chr12:30949084-30949863	SK-N-SH	brain:	n/a	chr12:30949342-30949351
4	MAX	chr12:30947908-30949830	ECC-1	luminal epithelium:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
5	MYC	chr12:30947587-30949584	NB4	blood:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
6	POLR2A	chr12:30947455-30950217	HUVEC	blood vessel:	n/a	n/a
7	ZBTB7A	chr12:30947681-30950078	ECC-1	luminal epithelium:	n/a	chr12:30948413-30948420
8	RCOR1	chr12:30947587-30949535	Hela-S3	cervix:	n/a	n/a
9	MAFK	chr12:30947721-30949552	Hela-S3	cervix:	n/a	chr12:30948077-30948086
10	POLR2A	chr12:30947518-30949699	U87	brain:	n/a	n/a
11	POLR2A	chr12:30947579-30950081	HUVEC	blood vessel:	n/a	n/a
12	ZBTB7A	chr12:30949022-30949620	K562	blood:	n/a	n/a
13	MAZ	chr12:30948947-30949675	HepG2	liver:	n/a	chr12:30949347-30949356
14	POLR2A	chr12:30947662-30949621	PANC-1	pancreas:	n/a	n/a
15	MYC	chr12:30947622-30949655	Hela-S3	cervix:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
16	FOXM1	chr12:30947622-30949535	ECC-1	luminal epithelium:	n/a	chr12:30948025-30948033
17	MAX	chr12:30947459-30950381	A549	lung:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
18	EGR1	chr12:30947585-30949597	HCT-116	colon:	n/a	chr12:30948109-30948118 chr12:30948106-30948119 chr12:30949166-30949180
19	POLR2A	chr12:30948099-30949636	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZKSCAN1	chr12:30947610-30949576	Hela-S3	cervix:	n/a	n/a
21	PBX3	chr12:30947711-30949544	SK-N-SH	brain:	n/a	n/a
22	ZNF263	chr12:30948167-30950323	HEK293-T-REx	kidney:	n/a	chr12:30949957-30949966
23	POLR2A	chr12:30948030-30949713	ECC-1	luminal epithelium:	n/a	n/a
24	YY1	chr12:30949300-30949633	SK-N-SH_RA	brain:	n/a	n/a
25	MAX	chr12:30947836-30949690	SK-N-SH	brain:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
26	POLR2A	chr12:30947727-30949517	NB4	blood:	n/a	n/a
27	POLR2A	chr12:30947330-30950355	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr12:30948002-30949714	ECC-1	luminal epithelium:	n/a	n/a
29	RAD21	chr12:30949007-30949550	SK-N-SH_RA	brain:	n/a	n/a
30	E2F6	chr12:30948328-30949714	H1-hESC	embryonic stem cell:	n/a	chr12:30949341-30949351 chr12:30949269-30949279 chr12:30949210-30949219 chr12:30948414-30948426
31	TBP	chr12:30947584-30950261	Hela-S3	cervix:	n/a	n/a
32	SRF	chr12:30947970-30949708	ECC-1	luminal epithelium:	n/a	n/a
33	RAD21	chr12:30947815-30949736	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr12:30947972-30949758	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr12:30947377-30950489	U87	brain:	n/a	n/a
36	PBX3	chr12:30947739-30949691	SK-N-SH	brain:	n/a	n/a
37	MAX	chr12:30947695-30949828	ECC-1	luminal epithelium:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
38	CREB1	chr12:30948038-30949721	A549	lung:	n/a	chr12:30948521-30948534
39	MAX	chr12:30947476-30949646	Hela-S3	cervix:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
40	POLR2A	chr12:30947604-30950324	IMR90	lung:	n/a	n/a
41	JUND	chr12:30947577-30949715	SK-N-SH	brain:	n/a	chr12:30948296-30948307 chr12:30948298-30948307 chr12:30948078-30948088 chr12:30948078-30948088 chr12:30948297-30948306 chr12:30948078-30948088 chr12:30948078-30948088
42	EP300	chr12:30947385-30949871	ECC-1	luminal epithelium:	n/a	chr12:30949342-30949351 chr12:30949708-30949717 chr12:30948297-30948306 chr12:30947657-30947667
43	POLR2A	chr12:30948072-30949651	ProgFib	skin:	n/a	n/a
44	YY1	chr12:30949088-30949528	SK-N-SH_RA	brain:	n/a	chr12:30949208-30949222
45	SMARCC1	chr12:30947538-30949652	Hela-S3	cervix:	n/a	chr12:30948297-30948306
46	NRF1	chr12:30949459-30949630	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr12:30947335-30949674	HUVEC	blood vessel:	n/a	n/a
48	E2F6	chr12:30949439-30949636	K562	blood:	n/a	n/a
49	TCF12	chr12:30947393-30949591	A549	lung:	n/a	chr12:30948696-30948706
50	JUND	chr12:30947851-30949598	H1-hESC	embryonic stem cell:	n/a	chr12:30948296-30948307 chr12:30948298-30948307 chr12:30948078-30948088 chr12:30948078-30948088 chr12:30948297-30948306 chr12:30948078-30948088 chr12:30948078-30948088

No.	Distal block	Cell Line	Cell type
1	chr12:30906304..30909589-chr12:30948532..30951386,3	K562	blood:
2	chr12:30949150..30949851-chr4:92369989..92370606,2	Hela-S3	cervix:
3	chr12:30949301..30951122-chr12:30954767..30957062,2	MCF-7	breast:
4	chr12:30949445..30950276-chr9:2015332..2016130,2	Hela-S3	cervix:

Variant related genes	Relation type
LINC00941	TF binding region
ENSG00000110888	Chromatin interaction
ENSG00000080503	Chromatin interaction
ENSG00000246331	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	0.88[EUR][1000 genomes]
rs166277	0.88[EUR][1000 genomes]
rs171760	0.86[EUR][1000 genomes]
rs187673	0.88[EUR][1000 genomes]
rs2352525	0.87[EUR][1000 genomes]
rs256656	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256657	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256661	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs256663	0.94[ASN][1000 genomes]
rs256665	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256666	0.90[EUR][1000 genomes]
rs256667	0.94[ASN][1000 genomes]
rs256669	0.90[EUR][1000 genomes]
rs256670	0.89[EUR][1000 genomes]
rs256671	0.90[EUR][1000 genomes]
rs256672	0.90[EUR][1000 genomes]
rs256673	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256674	0.90[EUR][1000 genomes]
rs256675	0.90[EUR][1000 genomes]
rs256676	0.90[EUR][1000 genomes]
rs256677	0.90[EUR][1000 genomes]
rs256679	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256680	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256681	0.91[EUR][1000 genomes]
rs256682	0.91[EUR][1000 genomes]
rs256683	0.91[EUR][1000 genomes]
rs256684	0.91[EUR][1000 genomes]
rs256685	0.91[EUR][1000 genomes]
rs256687	0.89[EUR][1000 genomes]
rs256689	0.91[EUR][1000 genomes]
rs256690	0.91[EUR][1000 genomes]
rs256692	0.91[EUR][1000 genomes]
rs256693	0.90[EUR][1000 genomes]
rs256694	0.91[EUR][1000 genomes]
rs256695	0.91[EUR][1000 genomes]
rs256696	0.88[EUR][1000 genomes]
rs256697	0.94[ASN][1000 genomes]
rs256698	0.86[EUR][1000 genomes]
rs256699	0.87[EUR][1000 genomes]
rs538731	0.90[EUR][1000 genomes]
rs73534	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]

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:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30947600-30950200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:30947800-30949800	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr12:30948000-30950000	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr12:30948000-30950000	Active TSS	Hela-S3	cervix
5	chr12:30948000-30950200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:30948000-30950400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr12:30948200-30949600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:30948200-30949800	Active TSS	Brain Angular Gyrus	brain
9	chr12:30948200-30949800	Active TSS	Right Atrium	heart
10	chr12:30948200-30950000	Active TSS	H9 Cell Line	embryonic stem cell
11	chr12:30948200-30950000	Bivalent Enhancer	Fetal Brain Male	brain
12	chr12:30948200-30950000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
13	chr12:30948200-30950400	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr12:30948200-30950400	Active TSS	Brain Anterior Caudate	brain
15	chr12:30948400-30949600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
16	chr12:30948400-30949600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
17	chr12:30948400-30949600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:30948400-30949600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr12:30948400-30949600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
20	chr12:30948400-30949600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
21	chr12:30948400-30949800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
22	chr12:30948400-30949800	Active TSS	Brain Substantia Nigra	brain
23	chr12:30948400-30949800	Bivalent/Poised TSS	Fetal Lung	lung
24	chr12:30948400-30949800	Active TSS	Left Ventricle	heart
25	chr12:30948400-30949800	Active TSS	Right Ventricle	heart
26	chr12:30948400-30950000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:30948400-30950000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
28	chr12:30948400-30950000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
29	chr12:30948400-30950000	Flanking Bivalent TSS/Enh	Placenta	Placenta
30	chr12:30948400-30950200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr12:30948400-30950200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:30948400-30950200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:30948400-30950200	Active TSS	Aorta	Aorta
34	chr12:30948400-30950200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
35	chr12:30948400-30950200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
36	chr12:30948400-30950200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
37	chr12:30948400-30950200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
38	chr12:30948400-30950200	Active TSS	HSMMtube	muscle
39	chr12:30948400-30950400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
40	chr12:30948400-30950400	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr12:30948600-30949600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:30948600-30949600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:30948600-30949600	Flanking Active TSS	Liver	Liver
44	chr12:30948600-30949600	Active TSS	Gastric	stomach
45	chr12:30948600-30949600	Flanking Active TSS	Psoas Muscle	Psoas
46	chr12:30948600-30949800	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr12:30948600-30949800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:30948600-30949800	Bivalent/Poised TSS	Fetal Brain Female	brain
49	chr12:30948600-30949800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
50	chr12:30948600-30949800	Active TSS	Fetal Kidney	kidney

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