Variant report

Variant	rs543850660
Chromosome Location	chr1:228675768-228675769
allele	C/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	POLR2A	chr1:228675488-228676933	PFSK-1	brain:	n/a	n/a
2	MYC	chr1:228674273-228675985	K562	blood:	n/a	chr1:228675761-228675771
3	POLR2A	chr1:228675579-228678949	K562	blood:	n/a	n/a
4	ZBTB7A	chr1:228675266-228675994	K562	blood:	n/a	n/a
5	POLR2A	chr1:228675691-228676901	U87	brain:	n/a	n/a
6	POLR2A	chr1:228675591-228676658	HCT-116	colon:	n/a	n/a
7	MAZ	chr1:228674322-228675843	Hela-S3	cervix:	n/a	chr1:228675761-228675771
8	UBTF	chr1:228674534-228676112	K562	blood:	n/a	n/a
9	POLR2A	chr1:228674145-228676899	K562	blood:	n/a	n/a
10	POLR2A	chr1:228675655-228675844	A549	lung:	n/a	n/a
11	MAX	chr1:228674235-228675954	HepG2	liver:	n/a	chr1:228675761-228675771
12	JUND	chr1:228675678-228675913	K562	blood:	n/a	n/a
13	POLR2A	chr1:228675668-228676339	U87	brain:	n/a	n/a
14	CTCF	chr1:228675105-228675789	K562	blood:	n/a	chr1:228675764-228675777 chr1:228675396-228675409 chr1:228675399-228675412
15	POLR2A	chr1:228674089-228676108	GM12892	blood:	n/a	n/a
16	MYC	chr1:228674297-228675857	NB4	blood:	n/a	chr1:228675761-228675771
17	POLR2A	chr1:228675570-228676460	HL-60	blood:	n/a	n/a
18	POLR2A	chr1:228674014-228675771	H1-neurons	neurons:	n/a	n/a
19	MAFK	chr1:228675733-228675820	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr1:228675616-228676024	MCF-7	breast:	n/a	n/a
21	POLR2A	chr1:228674228-228676223	GM19193	blood:	n/a	n/a
22	POLR2A	chr1:228674162-228676850	GM12878	blood:	n/a	n/a
23	E2F6	chr1:228674230-228675912	K562	blood:	n/a	chr1:228674560-228674575 chr1:228675503-228675513 chr1:228674565-228674572 chr1:228674565-228674572 chr1:228675473-228675488 chr1:228675168-228675178 chr1:228675173-228675182 chr1:228674565-228674572 chr1:228674563-228674574 chr1:228674564-228674573 chr1:228674564-228674576
24	UBTF	chr1:228674206-228676142	K562	blood:	n/a	n/a
25	YY1	chr1:228674374-228675870	K562	blood:	n/a	chr1:228675632-228675641 chr1:228675144-228675155 chr1:228675199-228675213 chr1:228675171-228675185 chr1:228675168-228675182 chr1:228675220-228675234 chr1:228675632-228675643 chr1:228675490-228675504 chr1:228675173-228675182 chr1:228675395-228675409
26	POLR2A	chr1:228674182-228676219	GM18526	blood:	n/a	n/a
27	POLR2A	chr1:228674187-228676212	GM18505	blood:	n/a	n/a
28	POLR2A	chr1:228675529-228676740	HCT-116	colon:	n/a	n/a
29	HMGN3	chr1:228674207-228675776	K562	blood:	n/a	n/a
30	POLR2A	chr1:228674181-228676169	A549	lung:	n/a	n/a
31	MYC	chr1:228674147-228676005	K562	blood:	n/a	chr1:228675761-228675771
32	MXI1	chr1:228673999-228676881	IMR90	lung:	n/a	n/a
33	POLR2A	chr1:228673803-228676876	HepG2	liver:	n/a	n/a
34	MAX	chr1:228674217-228675932	K562	blood:	n/a	chr1:228675761-228675771
35	BHLHE40	chr1:228675520-228675780	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:228675567-228676947	U87	brain:	n/a	n/a
37	POLR2A	chr1:228675707-228675776	Gliobla	brain:	n/a	n/a
38	POLR2A	chr1:228675618-228675997	ProgFib	skin:	n/a	n/a
39	GABPA	chr1:228674234-228675929	K562	blood:	n/a	chr1:228675176-228675185
40	RCOR1	chr1:228674188-228676026	K562	blood:	n/a	n/a
41	POLR2A	chr1:228675685-228675798	A549	lung:	n/a	n/a
42	CHD2	chr1:228675713-228676039	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr1:228675568-228676966	SK-N-MC	brain:	n/a	n/a
44	POLR2A	chr1:228675744-228675828	GM12878	blood:	n/a	n/a
45	YY1	chr1:228675659-228676033	GM12878	blood:	n/a	chr1:228675860-228675871
46	CTCF	chr1:228675720-228675870	GM12872	blood:	n/a	chr1:228675832-228675850 chr1:228675764-228675777 chr1:228675838-228675847
47	CTCF	chr1:228675745-228675884	GM12891	blood:	n/a	chr1:228675832-228675850 chr1:228675764-228675777 chr1:228675838-228675847
48	ZBTB7A	chr1:228675487-228675939	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr1:228675680-228676075	GM12878	blood:	n/a	n/a
50	POLR2A	chr1:228675746-228675901	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228290240..228293064-chr1:228675062..228676582,2	K562	blood:
2	chr1:228400032..228401961-chr1:228675104..228677391,2	MCF-7	breast:
3	chr1:228592366..228594573-chr1:228675027..228676697,3	MCF-7	breast:
4	chr1:11967567..11969704-chr1:228673208..228675906,2	MCF-7	breast:
5	chr1:228642342..228647806-chr1:228672380..228678428,13	MCF-7	breast:
6	chr1:228674158..228676652-chr1:228698714..228701340,3	K562	blood:
7	chr1:228675436..228678007-chr1:228697619..228700594,3	MCF-7	breast:
8	chr1:228671614..228676496-chr1:228676543..228681096,6	MCF-7	breast:
9	chr1:228672968..228678350-chr1:228679226..228685848,20	MCF-7	breast:
10	chr1:228487271..228488896-chr1:228674554..228676402,2	K562	blood:
11	chr1:228643230..228649256-chr1:228671672..228678578,15	MCF-7	breast:
12	chr1:24285294..24286180-chr1:228675458..228676219,2	HCT-116	colon:

Variant related genes	Relation type
RNF187	TF binding region
ENSG00000154358	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000154370	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000188822	Chromatin interaction
ENSG00000168159	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000215811	Chromatin interaction
ENSG00000189266	Chromatin interaction
ENSG00000162913	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	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
9	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
12	esv3417507	chr1:228673529-228677127	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	esv3338881	chr1:228674354-228676902	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
14	esv3408363	chr1:228674504-228676727	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr1:228673600-228675800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:228673600-228675800	Active TSS	K562	blood
3	chr1:228673600-228676000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:228673600-228676000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:228673600-228676000	Active TSS	A549	lung
6	chr1:228673600-228676000	Active TSS	Hela-S3	cervix
7	chr1:228673600-228676200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:228673800-228675800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:228673800-228675800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:228673800-228675800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:228673800-228675800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:228673800-228675800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:228673800-228675800	Active TSS	Brain Hippocampus Middle	brain
14	chr1:228673800-228675800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:228673800-228675800	Active TSS	Fetal Muscle Leg	muscle
16	chr1:228673800-228675800	Active TSS	GM12878-XiMat	blood
17	chr1:228673800-228676000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:228673800-228676000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:228673800-228676000	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr1:228673800-228676000	Active TSS	Primary T cells from cord blood	blood
21	chr1:228673800-228676000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:228673800-228676000	Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:228673800-228676000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:228673800-228676000	Active TSS	Aorta	Aorta
25	chr1:228673800-228676000	Active TSS	Brain Cingulate Gyrus	brain
26	chr1:228673800-228676000	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr1:228673800-228676000	Active TSS	Colon Smooth Muscle	Colon
28	chr1:228673800-228676000	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr1:228673800-228676000	Active TSS	Fetal Intestine Large	intestine
30	chr1:228673800-228676000	Active TSS	Psoas Muscle	Psoas
31	chr1:228673800-228676000	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr1:228673800-228676000	Active TSS	Rectal Smooth Muscle	rectum
33	chr1:228673800-228676000	Active TSS	NHEK	skin
34	chr1:228673800-228676200	Active TSS	Brain Angular Gyrus	brain
35	chr1:228673800-228676200	Active TSS	HSMM	muscle
36	chr1:228673800-228676200	Active TSS	NHLF	lung
37	chr1:228673800-228676600	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr1:228673800-228676600	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr1:228673800-228676800	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr1:228674000-228675800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:228674000-228675800	Active TSS	Primary hematopoietic stem cells	blood
42	chr1:228674000-228675800	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr1:228674000-228675800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr1:228674000-228675800	Active TSS	Brain Substantia Nigra	brain
45	chr1:228674000-228675800	Active TSS	Fetal Lung	lung
46	chr1:228674000-228675800	Active TSS	Gastric	stomach
47	chr1:228674000-228675800	Active TSS	Left Ventricle	heart
48	chr1:228674000-228675800	Active TSS	Lung	lung
49	chr1:228674000-228675800	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr1:228674000-228675800	Active TSS	Sigmoid Colon	Sigmoid Colon

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