Variant report

Variant	rs12741681
Chromosome Location	chr1:225997741-225997742
allele	A/C
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	YY1	chr1:225997555-225998313	ECC-1	luminal epithelium:	n/a	chr1:225997843-225997857 chr1:225997836-225997847 chr1:225997981-225997992
2	KAP1	chr1:225997504-225998214	HEK293	kidney:	n/a	n/a
3	SMC3	chr1:225997592-225998247	Hela-S3	cervix:	n/a	chr1:225998182-225998192 chr1:225998027-225998037
4	E2F6	chr1:225997644-225997939	K562	blood:	n/a	chr1:225997843-225997853 chr1:225997840-225997850
5	POLR2A	chr1:225997584-225998172	K562	blood:	n/a	n/a
6	POLR2A	chr1:225997494-225998107	HEK293	kidney:	n/a	n/a
7	POLR2A	chr1:225997512-225998264	Hela-S3	cervix:	n/a	n/a
8	TBP	chr1:225997527-225998197	K562	blood:	n/a	n/a
9	POLR2A	chr1:225997693-225997942	GM12878	blood:	n/a	n/a
10	IRF1	chr1:225997536-225998198	K562	blood:	n/a	n/a
11	TAF1	chr1:225997493-225998220	A549	lung:	n/a	n/a
12	POLR2A	chr1:225997492-225998203	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:225997702-225997955	GM12878	blood:	n/a	n/a
14	SIN3A	chr1:225997515-225998295	H1-hESC	embryonic stem cell:	n/a	chr1:225998027-225998040
15	GABPA	chr1:225997598-225998227	H1-hESC	embryonic stem cell:	n/a	n/a
16	RCOR1	chr1:225997407-225998254	K562	blood:	n/a	n/a
17	ZNF143	chr1:225997628-225998208	GM12878	blood:	n/a	chr1:225998068-225998086 chr1:225998011-225998020 chr1:225998013-225998022 chr1:225998039-225998049
18	YY1	chr1:225997546-225998124	HepG2	liver:	n/a	chr1:225997843-225997857 chr1:225997836-225997847 chr1:225997981-225997992
19	POLR2A	chr1:225997413-225998142	U87	brain:	n/a	n/a
20	MYC	chr1:225997682-225997787	MCF10A-Er-Src	breast:	n/a	n/a
21	RAD21	chr1:225997507-225998242	SK-N-SH_RA	brain:	n/a	chr1:225998027-225998037 chr1:225998182-225998192
22	TEAD4	chr1:225997527-225997925	K562	blood:	n/a	n/a
23	POLR2A	chr1:225997533-225998219	K562	blood:	n/a	n/a
24	SP1	chr1:225997452-225998218	A549	lung:	n/a	n/a
25	RAD21	chr1:225997525-225998250	H1-hESC	embryonic stem cell:	n/a	chr1:225998027-225998037 chr1:225998182-225998192
26	POLR2A	chr1:225997686-225997937	HepG2	liver:	n/a	n/a
27	MXI1	chr1:225997193-225998332	IMR90	lung:	n/a	n/a
28	POLR2A	chr1:225997638-225998443	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr1:225997582-225998271	Hela-S3	cervix:	n/a	n/a
30	MAX	chr1:225997561-225998226	K562	blood:	n/a	n/a
31	POLR2A	chr1:225997445-225997978	HepG2	liver:	n/a	n/a
32	REST	chr1:225997330-225999216	H1-neurons	neurons:	n/a	n/a
33	GTF2F1	chr1:225997526-225997997	Hela-S3	cervix:	n/a	n/a
34	TAF1	chr1:225997577-225998007	K562	blood:	n/a	n/a
35	E2F4	chr1:225997517-225998218	MCF10A-Er-Src	breast:	n/a	chr1:225997843-225997853 chr1:225997840-225997850
36	YY1	chr1:225997610-225998250	K562	blood:	n/a	chr1:225997843-225997857 chr1:225997836-225997847 chr1:225997981-225997992
37	TAF1	chr1:225997522-225998093	MCF-7	breast:	n/a	n/a
38	POLR2A	chr1:225997648-225998346	H1-neurons	neurons:	n/a	n/a
39	POLR2A	chr1:225997556-225998203	A549	lung:	n/a	n/a
40	MAZ	chr1:225997591-225998252	K562	blood:	n/a	n/a
41	RAD21	chr1:225997585-225998229	IMR90	lung:	n/a	chr1:225998027-225998037 chr1:225998182-225998192
42	PAX5	chr1:225997675-225998017	GM12892	blood:	n/a	n/a
43	RCOR1	chr1:225997542-225997845	K562	blood:	n/a	n/a
44	POLR2A	chr1:225997655-225997974	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr1:225997379-225998099	PFSK-1	brain:	n/a	n/a
46	POLR2A	chr1:225997523-225997981	HepG2	liver:	n/a	n/a
47	POLR2A	chr1:225997503-225998278	ECC-1	luminal epithelium:	n/a	n/a
48	MYC	chr1:225997606-225998254	K562	blood:	n/a	n/a
49	FOXP2	chr1:225997667-225997894	SK-N-MC	brain:	n/a	n/a
50	TCF7L2	chr1:225997537-225997833	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:225962862..225967352-chr1:225996084..226002774,11	MCF-7	breast:
2	chr1:225989164..225991391-chr1:225995297..225997953,3	K562	blood:
3	chr1:225962294..225967531-chr1:225994011..226002080,11	K562	blood:
4	chr1:225997407..225998221-chr13:111367411..111367928,2	Hela-S3	cervix:
5	chr1:225963904..225970275-chr1:225994893..226001084,15	K562	blood:
6	chr1:225963814..225970754-chr1:225996230..226002908,14	MCF-7	breast:
7	chr1:225995407..225997753-chr1:226172864..226175325,2	K562	blood:

Variant related genes	Relation type
EPHX1	TF binding region
ENSG00000153487	Chromatin interaction
ENSG00000234112	Chromatin interaction
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10737418	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10737419	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10737420	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10753409	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10799323	0.84[EUR][1000 genomes]
rs10799324	0.98[ASN][1000 genomes]
rs10915877	0.89[EUR][1000 genomes]
rs10915878	0.83[ASN][1000 genomes]
rs11808973	0.88[EUR][1000 genomes]
rs12727007	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12744609	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12757220	0.83[EUR][1000 genomes]
rs1467143	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4559463	0.82[ASN][1000 genomes]
rs4653436	0.83[ASN][1000 genomes]
rs4653679	0.81[EUR][1000 genomes]
rs4653684	0.88[EUR][1000 genomes]
rs4653685	0.88[EUR][1000 genomes]
rs4653686	0.88[EUR][1000 genomes]
rs4653688	0.83[ASN][1000 genomes]
rs55736073	0.83[ASN][1000 genomes]
rs57440270	0.83[ASN][1000 genomes]
rs58241471	0.83[ASN][1000 genomes]
rs6426089	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6687036	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv945327	chr1:225991086-225998770	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 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	chr1:225979600-225997800	Weak transcription	Gastric	stomach
2	chr1:225986000-225998000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:225997200-225998000	Active TSS	HMEC	breast
4	chr1:225997200-225998400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:225997200-225998400	Active TSS	HSMMtube	muscle
6	chr1:225997200-225998600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:225997200-225998600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:225997200-225998600	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr1:225997200-225998600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr1:225997200-225998600	Active TSS	Hela-S3	cervix
11	chr1:225997200-225998600	Active TSS	HSMM	muscle
12	chr1:225997200-225998800	Active TSS	Osteobl	bone
13	chr1:225997200-225999000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:225997200-225999000	Active TSS	Brain Hippocampus Middle	brain
15	chr1:225997200-225999200	Active TSS	Brain Angular Gyrus	brain
16	chr1:225997200-225999200	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr1:225997200-225999200	Active TSS	Rectal Smooth Muscle	rectum
18	chr1:225997200-225999600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:225997400-225997800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:225997400-225997800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr1:225997400-225997800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr1:225997400-225997800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
23	chr1:225997400-225997800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
24	chr1:225997400-225997800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr1:225997400-225997800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr1:225997400-225997800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:225997400-225997800	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr1:225997400-225997800	Flanking Active TSS	Fetal Muscle Trunk	muscle
29	chr1:225997400-225997800	Enhancers	Lung	lung
30	chr1:225997400-225998000	Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr1:225997400-225998200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:225997400-225998200	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr1:225997400-225998200	Active TSS	Rectal Mucosa Donor 31	rectum
34	chr1:225997400-225998400	Active TSS	Primary T cells from cord blood	blood
35	chr1:225997400-225998400	Flanking Active TSS	Dnd41	blood
36	chr1:225997400-225998400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr1:225997400-225998600	Active TSS	H1 Cell Line	embryonic stem cell
38	chr1:225997400-225998600	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr1:225997400-225998600	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr1:225997400-225998600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:225997400-225998600	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr1:225997400-225998600	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr1:225997400-225998600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:225997400-225998600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:225997400-225998600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:225997400-225998600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:225997400-225998600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:225997400-225998600	Active TSS	Brain Substantia Nigra	brain
49	chr1:225997400-225998600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr1:225997400-225998600	Active TSS	Fetal Muscle Leg	muscle

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