Variant report

Variant	rs12407568
Chromosome Location	chr1:228783329-228783330
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	MYC	chr1:228783294-228784072	MCF10A-Er-Src	breast:	n/a	n/a
2	HA-E2F1	chr1:228782952-228784102	MCF-7	breast:	n/a	chr1:228783805-228783812 chr1:228783095-228783105 chr1:228783096-228783107 chr1:228783096-228783104 chr1:228783095-228783106 chr1:228783943-228783952 chr1:228783084-228783098 chr1:228783096-228783103 chr1:228783384-228783396 chr1:228783096-228783104
3	TAF1	chr1:228783205-228783626	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr1:228783272-228784010	A549	lung:	n/a	n/a
5	RCOR1	chr1:228783243-228783426	GM12878	blood:	n/a	n/a
6	STAT3	chr1:228783300-228783743	MCF10A-Er-Src	breast:	n/a	chr1:228783635-228783643 chr1:228783309-228783321
7	TAF1	chr1:228783281-228783975	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:228782399-228784218	Hela-S3	cervix:	n/a	n/a
9	MAX	chr1:228782936-228784291	MCF-7	breast:	n/a	chr1:228784239-228784249
10	POLR2A	chr1:228783298-228783608	SK-N-SH	brain:	n/a	n/a
11	SIX5	chr1:228783208-228784208	A549	lung:	n/a	n/a
12	SETDB1	chr1:228783197-228784162	U2OS	brain:	n/a	n/a
13	ZNF143	chr1:228783243-228783983	Hela-S3	cervix:	n/a	n/a
14	FOXP2	chr1:228783267-228783646	PFSK-1	brain:	n/a	n/a
15	REST	chr1:228783245-228783868	PANC-1	pancreas:	n/a	chr1:228783513-228783526
16	HEY1	chr1:228783149-228783795	HepG2	liver:	n/a	n/a
17	SMARCB1	chr1:228782483-228784310	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:228782420-228783936	HepG2	liver:	n/a	n/a
19	GATA3	chr1:228783064-228784303	A549	lung:	n/a	n/a
20	MAX	chr1:228782455-228784026	ECC-1	luminal epithelium:	n/a	n/a
21	SIX5	chr1:228783159-228783628	A549	lung:	n/a	n/a
22	MYC	chr1:228783258-228784112	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr1:228783211-228784022	HepG2	liver:	n/a	n/a
24	POLR2A	chr1:228782343-228784099	Hela-S3	cervix:	n/a	n/a
25	SIN3AK20	chr1:228783096-228784253	MCF-7	breast:	n/a	n/a
26	GATA3	chr1:228783311-228784203	MCF-7	breast:	n/a	n/a
27	POLR2A	chr1:228782361-228784289	Hela-S3	cervix:	n/a	n/a
28	SIN3AK20	chr1:228783294-228783615	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:228782416-228784035	GM15510	blood:	n/a	n/a
30	POLR2A	chr1:228782354-228783551	NB4	blood:	n/a	n/a
31	ATF3	chr1:228783161-228783846	A549	lung:	n/a	n/a
32	TAF1	chr1:228783013-228784232	A549	lung:	n/a	n/a
33	TCF7L2	chr1:228782917-228784324	Hela-S3	cervix:	n/a	n/a
34	MYBL2	chr1:228783306-228783970	HepG2	liver:	n/a	n/a
35	ELK1	chr1:228783119-228783766	Hela-S3	cervix:	n/a	n/a
36	MAZ	chr1:228782572-228783886	Hela-S3	cervix:	n/a	n/a
37	E2F6	chr1:228782547-228784030	A549	lung:	n/a	chr1:228783805-228783812 chr1:228783095-228783105 chr1:228783096-228783107 chr1:228783096-228783104 chr1:228783095-228783106 chr1:228783943-228783952 chr1:228783084-228783098 chr1:228783096-228783103 chr1:228783384-228783396 chr1:228783096-228783104
38	CHD2	chr1:228782398-228784265	Hela-S3	cervix:	n/a	chr1:228783099-228783109 chr1:228783311-228783321 chr1:228783805-228783812
39	TBP	chr1:228782430-228785001	Hela-S3	cervix:	n/a	n/a
40	NFIC	chr1:228783292-228783630	HepG2	liver:	n/a	n/a
41	RCOR1	chr1:228782490-228783979	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr1:228782755-228784050	A549	lung:	n/a	n/a
43	POLR2A	chr1:228782342-228784357	Hela-S3	cervix:	n/a	n/a
44	MAX	chr1:228782832-228784338	HepG2	liver:	n/a	chr1:228784239-228784249
45	KAP1	chr1:228783290-228784071	U2OS	brain:	n/a	n/a
46	YY1	chr1:228783240-228783642	A549	lung:	n/a	n/a
47	CTBP2	chr1:228782732-228784117	H1-hESC	embryonic stem cell:	n/a	n/a
48	SP1	chr1:228781284-228784045	A549	lung:	n/a	chr1:228782216-228782226 chr1:228782343-228782353 chr1:228782780-228782794 chr1:228782216-228782226
49	E2F4	chr1:228783230-228784174	MCF10A-Er-Src	breast:	n/a	chr1:228783805-228783812 chr1:228783943-228783952 chr1:228783384-228783396
50	POLR2A	chr1:228783103-228784099	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228783048..228783985-chr16:3070059..3070679,2	HCT-116	colon:
2	chr1:228783138..228784040-chr9:140135254..140135781,2	HCT-116	colon:
3	chr1:228783070..228784014-chr12:123011279..123011841,2	Hela-S3	cervix:
4	chr1:17231506..17232339-chr1:228782832..228783652,2	Hela-S3	cervix:
5	chr1:228782241..228785119-chr1:228785249..228788137,2	K562	blood:
6	chr1:228783073..228784051-chr7:5569241..5569745,2	Hela-S3	cervix:

Variant related genes	Relation type
RNA5S16	TF binding region
DUSP5P1	TF binding region
ENSG00000206878	TF binding region
RNA5S17	TF binding region
ENSG00000075624	Chromatin interaction
ENSG00000006327	Chromatin interaction
ENSG00000183929	Chromatin interaction
ENSG00000184445	Chromatin interaction
ENSG00000111011	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000184697	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10753451	0.91[ASN][1000 genomes]
rs10753452	0.87[ASN][1000 genomes]
rs10916338	0.87[ASN][1000 genomes]
rs12028431	0.89[ASN][1000 genomes]
rs12034519	1.00[EUR][1000 genomes]
rs12035708	0.91[ASN][1000 genomes]
rs12140890	0.89[ASN][1000 genomes]
rs1925714	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1925717	0.85[ASN][1000 genomes]
rs1925721	0.87[ASN][1000 genomes]
rs1925722	0.80[ASN][1000 genomes]
rs2182200	0.89[ASN][1000 genomes]
rs35598069	0.98[ASN][1000 genomes]
rs35724040	0.98[ASN][1000 genomes]
rs4147255	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4147256	0.87[ASN][1000 genomes]
rs4653977	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4653979	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6426507	0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6670856	0.87[ASN][1000 genomes]
rs728964	0.89[ASN][1000 genomes]
rs7415895	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs744668	0.87[ASN][1000 genomes]
rs7533560	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv827075	chr1:228716554-228783674	Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
4	nsv945355	chr1:228716611-228784016	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	29 gene(s)	inside rSNPs	diseases
5	esv19715	chr1:228742638-228783674	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
6	esv3425415	chr1:228742829-228783527	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
7	nsv820567	chr1:228742962-228783403	Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
8	nsv827097	chr1:228742962-228783403	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
9	esv3331974	chr1:228743029-228783527	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
10	esv3342484	chr1:228743029-228783527	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
11	esv3382956	chr1:228743029-228783527	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
12	esv3445359	chr1:228743029-228783527	Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
13	esv3450984	chr1:228743029-228783527	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
14	esv1828070	chr1:228758016-228793246	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228782400-228783400	Flanking Bivalent TSS/Enh	Liver	Liver
2	chr1:228782400-228783800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:228782400-228783800	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
4	chr1:228782400-228784000	Flanking Bivalent TSS/Enh	Dnd41	blood
5	chr1:228782400-228784200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:228782400-228784200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:228782400-228784200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
9	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
10	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
11	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
12	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
14	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
15	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
16	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
17	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
18	chr1:228782400-228784200	Flanking Active TSS	Pancreas	Pancrea
19	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
20	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
21	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
22	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
23	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
24	chr1:228782400-228784400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr1:228782400-228784400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:228782400-228784400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
27	chr1:228782400-228784400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:228782400-228784400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
29	chr1:228782400-228784400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
32	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
33	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
34	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
37	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
38	chr1:228782400-228784600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:228782400-228784600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:228782400-228784600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:228782400-228784600	Active TSS	A549	lung
42	chr1:228782400-228785000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
43	chr1:228782400-228785000	Active TSS	Hela-S3	cervix
44	chr1:228782600-228783400	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
45	chr1:228782600-228783600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:228782600-228783600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
47	chr1:228782600-228783600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
48	chr1:228782600-228783800	Bivalent/Poised TSS	Fetal Kidney	kidney
49	chr1:228782600-228783800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
50	chr1:228782600-228783800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood

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