Variant report

Variant	rs12317077
Chromosome Location	chr12:51441587-51441588
allele	C/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	chr12:51441512-51442395	GM12891	blood:	n/a	n/a
2	MYC	chr12:51441539-51443099	K562	blood:	n/a	n/a
3	CTCF	chr12:51441534-51441823	T-47D	breast:	n/a	chr12:51441681-51441697 chr12:51441682-51441703 chr12:51441680-51441698
4	REST	chr12:51441544-51441796	PANC-1	pancreas:	n/a	chr12:51441654-51441663
5	HCFC1	chr12:51441461-51442350	K562	blood:	n/a	n/a
6	CTCF	chr12:51441580-51441730	HFF	foreskin:	n/a	chr12:51441681-51441697 chr12:51441682-51441703 chr12:51441680-51441698
7	ELF1	chr12:51441465-51442435	GM12878	blood:	n/a	chr12:51441932-51441943
8	POLR2A	chr12:51441408-51442365	ECC-1	luminal epithelium:	n/a	n/a
9	TBL1XR1	chr12:51441433-51442333	K562	blood:	n/a	n/a
10	EP300	chr12:51441537-51442120	SK-N-SH_RA	brain:	n/a	n/a
11	ELF1	chr12:51441490-51442319	A549	lung:	n/a	chr12:51441932-51441943
12	SMARCC2	chr12:51441503-51442520	Hela-S3	cervix:	n/a	n/a
13	EP300	chr12:51441301-51442444	A549	lung:	n/a	n/a
14	RAD21	chr12:51441486-51441925	GM12878	blood:	n/a	chr12:51441681-51441700 chr12:51441852-51441864 chr12:51441711-51441725
15	TAF1	chr12:51441458-51442470	MCF-7	breast:	n/a	n/a
16	ZNF143	chr12:51441511-51442166	H1-hESC	embryonic stem cell:	n/a	chr12:51441788-51441798 chr12:51441755-51441773
17	POLR2A	chr12:51441525-51442482	ProgFib	skin:	n/a	n/a
18	POLR2A	chr12:51441567-51442204	H1-hESC	embryonic stem cell:	n/a	n/a
19	RFX5	chr12:51441479-51442757	GM12878	blood:	n/a	n/a
20	CTCF	chr12:51441565-51441848	Kidney_OC	kidney:	n/a	chr12:51441681-51441697 chr12:51441682-51441703 chr12:51441680-51441698
21	POLR2A	chr12:51441369-51442373	SK-N-SH	brain:	n/a	n/a
22	TCF12	chr12:51441324-51442548	ECC-1	luminal epithelium:	n/a	chr12:51442366-51442374
23	TEAD4	chr12:51441549-51441874	H1-hESC	embryonic stem cell:	n/a	n/a
24	SP1	chr12:51441465-51442242	GM12878	blood:	n/a	n/a
25	NR2F2	chr12:51441370-51443056	MCF-7	breast:	n/a	n/a
26	PML	chr12:51441563-51442333	GM12878	blood:	n/a	n/a
27	CHD2	chr12:51441538-51442202	HepG2	liver:	n/a	chr12:51441923-51441930
28	POLR2A	chr12:51441342-51442962	GM12892	blood:	n/a	n/a
29	CTCF	chr12:51441552-51441869	Lung_OC	lung:	n/a	chr12:51441681-51441697 chr12:51441682-51441703 chr12:51441680-51441698
30	CHD2	chr12:51441473-51442849	GM12878	blood:	n/a	chr12:51441923-51441930
31	SMARCB1	chr12:51441459-51442607	Hela-S3	cervix:	n/a	n/a
32	SIN3AK20	chr12:51441442-51442369	SK-N-SH	brain:	n/a	n/a
33	TBL1XR1	chr12:51441518-51442289	GM12878	blood:	n/a	n/a
34	TAF1	chr12:51441369-51442746	ECC-1	luminal epithelium:	n/a	n/a
35	BCL3	chr12:51441389-51442561	A549	lung:	n/a	n/a
36	CTCF	chr12:51441580-51441730	HRE	kidney:	n/a	chr12:51441681-51441697 chr12:51441682-51441703 chr12:51441680-51441698
37	RAD21	chr12:51441507-51441906	H1-hESC	embryonic stem cell:	n/a	chr12:51441681-51441700 chr12:51441852-51441864 chr12:51441711-51441725
38	ELF1	chr12:51441575-51442169	HepG2	liver:	n/a	chr12:51441932-51441943
39	NFIC	chr12:51441527-51442268	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:51441434-51442741	K562	blood:	n/a	n/a
41	CTCF	chr12:51441545-51441861	Fibrobl	skin:	n/a	chr12:51441681-51441697 chr12:51441682-51441703 chr12:51441680-51441698
42	CTCF	chr12:51441580-51441730	A549	lung:	n/a	chr12:51441681-51441697 chr12:51441682-51441703 chr12:51441680-51441698
43	CTCF	chr12:51441581-51441802	GM20000	blood:	n/a	chr12:51441681-51441697 chr12:51441682-51441703 chr12:51441680-51441698
44	REST	chr12:51441364-51442406	PFSK-1	brain:	n/a	chr12:51441654-51441663
45	POLR2A	chr12:51441380-51442918	K562	blood:	n/a	n/a
46	POLR2A	chr12:51441256-51443160	SK-N-MC	brain:	n/a	n/a
47	TCF12	chr12:51441343-51442728	A549	lung:	n/a	chr12:51442366-51442374
48	MXI1	chr12:51441508-51442768	Hela-S3	cervix:	n/a	n/a
49	BCL3	chr12:51441541-51442475	A549	lung:	n/a	n/a
50	CTCF	chr12:51441580-51441730	Caco-2	colon:	n/a	chr12:51441681-51441697 chr12:51441682-51441703 chr12:51441680-51441698

No.	Distal block	Cell Line	Cell type
1	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
2	chr12:51441478..51442324-chr3:148847457..148848341,2	Hela-S3	cervix:
3	chr12:51440622..51443141-chr12:51753837..51755674,2	MCF-7	breast:
4	chr12:51440322..51443098-chr12:51662230..51665433,4	K562	blood:
5	chr12:51440588..51444188-chr12:51475693..51478745,10	K562	blood:
6	chr12:51440271..51447226-chr12:51475135..51479930,16	MCF-7	breast:
7	chr12:51440439..51443022-chr12:51565659..51567306,3	K562	blood:
8	chr12:31478566..31479069-chr12:51441568..51442472,2	NB4	blood:
9	chr12:51418602..51423346-chr12:51439309..51444851,15	MCF-7	breast:
10	chr12:51440619..51442939-chr12:51783521..51786364,2	MCF-7	breast:
11	chr12:51439067..51445190-chr12:51449547..51456560,11	K562	blood:
12	chr12:51440784..51442942-chr12:51664189..51666029,2	MCF-7	breast:
13	chr12:51440111..51442560-chr12:51783834..51785722,2	MCF-7	breast:
14	chr12:51429499..51431522-chr12:51440148..51442114,3	MCF-7	breast:
15	chr12:49658597..49659188-chr12:51441443..51442076,2	Hela-S3	cervix:
16	chr12:51440642..51443592-chr12:51616961..51619958,3	MCF-7	breast:
17	chr12:51156477..51159239-chr12:51440349..51444629,5	K562	blood:
18	chr12:51441202..51443113-chr12:51468336..51471322,2	K562	blood:
19	chr12:51421636..51422560-chr12:51441327..51442402,4	MCF-7	breast:
20	chr12:51440743..51444863-chr12:51448295..51453075,7	MCF-7	breast:
21	chr12:51440639..51443821-chr12:51630707..51634068,3	K562	blood:
22	chr12:51399373..51401239-chr12:51441069..51443548,3	MCF-7	breast:
23	chr12:51441021..51443304-chr12:51610017..51612719,2	MCF-7	breast:
24	chr12:51416659..51422801-chr12:51440164..51444812,17	MCF-7	breast:
25	chr12:51440554..51443122-chr12:51610984..51612842,2	K562	blood:
26	chr12:51440782..51445752-chr12:51631445..51635429,5	MCF-7	breast:
27	chr12:51441033..51441729-chr12:51640254..51641009,2	K562	blood:
28	chr12:51440588..51444188-chr12:51475774..51478819,7	K562	blood:
29	chr12:51440852..51445521-chr12:51475730..51478507,6	MCF-7	breast:
30	chr12:51419291..51420223-chr12:51441428..51442247,3	MCF-7	breast:
31	chr12:51419574..51420267-chr12:51441420..51442175,2	Hela-S3	cervix:

Variant related genes	Relation type
LETMD1	TF binding region
ENSG00000167553	Chromatin interaction
ENSG00000269339	Chromatin interaction
ENSG00000139629	Chromatin interaction
ENSG00000163755	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000170545	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000199903	Chromatin interaction
ENSG00000139146	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000135457	Chromatin interaction
ENSG00000050438	Chromatin interaction
ENSG00000184271	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10082984	1.00[AMR][1000 genomes]
rs11169699	1.00[AMR][1000 genomes]
rs12297361	1.00[AMR][1000 genomes]
rs12304202	1.00[AMR][1000 genomes]
rs12304653	1.00[AMR][1000 genomes]
rs12305543	1.00[AMR][1000 genomes]
rs12307922	1.00[AMR][1000 genomes]
rs12311001	1.00[AMR][1000 genomes]
rs12312957	1.00[AMR][1000 genomes]
rs12316887	1.00[AMR][1000 genomes]
rs12317980	1.00[AMR][1000 genomes]
rs12318042	1.00[AMR][1000 genomes]
rs12318187	1.00[AMR][1000 genomes]
rs12318936	1.00[AMR][1000 genomes]
rs17216086	1.00[AMR][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51440800-51441600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:51440800-51441600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
3	chr12:51440800-51441600	Flanking Active TSS	Dnd41	blood
4	chr12:51440800-51442600	Active TSS	Stomach Smooth Muscle	stomach
5	chr12:51440800-51442800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:51441000-51441600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:51441000-51441600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:51441000-51441600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:51441000-51441600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:51441000-51441600	Flanking Active TSS	Liver	Liver
11	chr12:51441000-51441600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr12:51441000-51441600	Enhancers	Spleen	Spleen
13	chr12:51441000-51441800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr12:51441000-51442400	Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr12:51441000-51442400	Active TSS	Brain Angular Gyrus	brain
16	chr12:51441000-51442400	Active TSS	Osteobl	bone
17	chr12:51441000-51442600	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr12:51441000-51442600	Active TSS	NHDF-Ad	bronchial
19	chr12:51441000-51443200	Active TSS	A549	lung
20	chr12:51441000-51443400	Active TSS	GM12878-XiMat	blood
21	chr12:51441000-51443600	Active TSS	Psoas Muscle	Psoas
22	chr12:51441200-51441600	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr12:51441200-51441600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:51441200-51441600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr12:51441200-51441600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:51441200-51441600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr12:51441200-51441600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr12:51441200-51441600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:51441200-51441600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:51441200-51441600	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr12:51441200-51441600	Flanking Active TSS	Brain Substantia Nigra	brain
32	chr12:51441200-51441600	Flanking Active TSS	Fetal Muscle Trunk	muscle
33	chr12:51441200-51441600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr12:51441200-51441600	Flanking Active TSS	NHEK	skin
35	chr12:51441200-51441800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr12:51441200-51441800	Active TSS	Brain Germinal Matrix	brain
37	chr12:51441200-51442200	Active TSS	HepG2	liver
38	chr12:51441200-51442400	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr12:51441200-51442400	Active TSS	Brain Cingulate Gyrus	brain
40	chr12:51441200-51442400	Active TSS	Rectal Smooth Muscle	rectum
41	chr12:51441200-51442600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:51441200-51442600	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr12:51441200-51442600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:51441200-51442600	Active TSS	Primary T cells from cord blood	blood
45	chr12:51441200-51442600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:51441200-51442600	Active TSS	Brain Anterior Caudate	brain
47	chr12:51441200-51442600	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr12:51441200-51442600	Active TSS	Fetal Brain Female	brain
49	chr12:51441200-51442600	Active TSS	HSMM	muscle
50	chr12:51441200-51442800	Active TSS	ES-I3 Cell Line	embryonic stem cell

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