Variant report

Variant	rs558020803
Chromosome Location	chr1:228270506-228270507
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	RUNX3	chr1:228269804-228270614	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:228269815-228272522	GM12892	blood:	n/a	n/a
3	HEY1	chr1:228270027-228270607	HepG2	liver:	n/a	chr1:228270374-228270389
4	GTF2F1	chr1:228270003-228270584	K562	blood:	n/a	n/a
5	RCOR1	chr1:228270012-228270529	Hela-S3	cervix:	n/a	n/a
6	MYC	chr1:228269812-228270766	MCF10A-Er-Src	breast:	n/a	chr1:228269970-228269981 chr1:228270033-228270043 chr1:228269970-228269980 chr1:228269972-228269979
7	HMGN3	chr1:228269758-228271532	K562	blood:	n/a	n/a
8	POLR2A	chr1:228269908-228270822	U87	brain:	n/a	n/a
9	TAF1	chr1:228269962-228270742	H1-hESC	embryonic stem cell:	n/a	n/a
10	YY1	chr1:228269771-228271394	HepG2	liver:	n/a	chr1:228270281-228270290 chr1:228270413-228270421 chr1:228270415-228270423 chr1:228270279-228270293 chr1:228269868-228269879 chr1:228270412-228270422
11	POLR2A	chr1:228268950-228270812	GM12891	blood:	n/a	n/a
12	EP300	chr1:228269990-228270593	HepG2	liver:	n/a	chr1:228270254-228270270 chr1:228270164-228270177
13	POLR2A	chr1:228269198-228271877	GM19193	blood:	n/a	n/a
14	SP1	chr1:228270081-228270510	GM12878	blood:	n/a	chr1:228270280-228270294 chr1:228270279-228270291 chr1:228270333-228270344 chr1:228270263-228270272 chr1:228270279-228270290 chr1:228270280-228270289 chr1:228270281-228270290 chr1:228270280-228270290 chr1:228270225-228270238 chr1:228270280-228270290 chr1:228270279-228270291 chr1:228270352-228270364 chr1:228270280-228270289 chr1:228270352-228270363
15	MXI1	chr1:228269786-228272826	IMR90	lung:	n/a	chr1:228269970-228269979
16	SP1	chr1:228269951-228270572	A549	lung:	n/a	chr1:228270280-228270294 chr1:228270279-228270291 chr1:228270333-228270344 chr1:228270263-228270272 chr1:228270279-228270290 chr1:228270280-228270289 chr1:228270281-228270290 chr1:228270280-228270290 chr1:228270225-228270238 chr1:228270280-228270290 chr1:228270279-228270291 chr1:228270352-228270364 chr1:228270280-228270289 chr1:228270352-228270363
17	POLR2A	chr1:228269793-228270676	HCT-116	colon:	n/a	n/a
18	YY1	chr1:228270140-228270863	ECC-1	luminal epithelium:	n/a	chr1:228270281-228270290 chr1:228270413-228270421 chr1:228270415-228270423 chr1:228270279-228270293 chr1:228270412-228270422
19	MAX	chr1:228269761-228270803	ECC-1	luminal epithelium:	n/a	chr1:228269763-228269773 chr1:228269970-228269981 chr1:228270033-228270043 chr1:228269970-228269980 chr1:228269972-228269979
20	MAX	chr1:228269375-228270644	H1-hESC	embryonic stem cell:	n/a	chr1:228269763-228269773 chr1:228269970-228269981 chr1:228270033-228270043 chr1:228269970-228269980 chr1:228269972-228269979
21	SIN3AK20	chr1:228270283-228270641	H1-hESC	embryonic stem cell:	n/a	n/a
22	GTF2F1	chr1:228270020-228270616	H1-hESC	embryonic stem cell:	n/a	n/a
23	IRF1	chr1:228270022-228270570	K562	blood:	n/a	chr1:228270350-228270364 chr1:228270277-228270291
24	TAF1	chr1:228270314-228270520	Hela-S3	cervix:	n/a	n/a
25	TAF1	chr1:228269811-228270592	A549	lung:	n/a	n/a
26	TAF1	chr1:228270264-228270585	GM12878	blood:	n/a	n/a
27	CEBPD	chr1:228269981-228270592	K562	blood:	n/a	n/a
28	POLR2A	chr1:228269908-228270854	U87	brain:	n/a	n/a
29	SMARCB1	chr1:228269838-228271805	Hela-S3	cervix:	n/a	n/a
30	EP300	chr1:228269989-228270518	GM12878	blood:	n/a	chr1:228270254-228270270 chr1:228270164-228270177
31	CREB1	chr1:228269350-228271910	HepG2	liver:	n/a	chr1:228270390-228270403
32	NRF1	chr1:228269936-228270515	GM12878	blood:	n/a	chr1:228270308-228270322 chr1:228270217-228270228 chr1:228270375-228270384 chr1:228270205-228270216 chr1:228270204-228270215 chr1:228270281-228270290 chr1:228270205-228270219
33	REST	chr1:228270138-228270571	HepG2	liver:	n/a	chr1:228270280-228270293
34	JUND	chr1:228270281-228270543	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:228268843-228274035	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:228269847-228270827	MCF-7	breast:	n/a	n/a
37	POLR2A	chr1:228269867-228272065	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr1:228269089-228271196	Raji	blood:	n/a	n/a
39	YY1	chr1:228270054-228270769	H1-hESC	embryonic stem cell:	n/a	chr1:228270281-228270290 chr1:228270413-228270421 chr1:228270415-228270423 chr1:228270279-228270293 chr1:228270412-228270422
40	POLR2A	chr1:228269858-228270814	MCF-7	breast:	n/a	n/a
41	FOS	chr1:228270011-228271057	HUVEC	blood vessel:	n/a	n/a
42	HCFC1	chr1:228269925-228270894	K562	blood:	n/a	n/a
43	POLR2A	chr1:228269831-228272124	PFSK-1	brain:	n/a	n/a
44	IRF1	chr1:228270013-228270892	K562	blood:	n/a	chr1:228270350-228270364 chr1:228270277-228270291
45	TCF3	chr1:228270382-228270529	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:228269854-228270786	H1-neurons	neurons:	n/a	n/a
47	MAX	chr1:228269736-228270584	K562	blood:	n/a	chr1:228269763-228269773 chr1:228269970-228269981 chr1:228270033-228270043 chr1:228269970-228269980 chr1:228269972-228269979
48	POLR2A	chr1:228269537-228270951	GM10847	blood:	n/a	n/a
49	POLR2A	chr1:228269729-228271211	A549	lung:	n/a	n/a
50	POLR2A	chr1:228269951-228271775	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:228270483-228270533	HNPCEpiC	eye:	n/a
2	chr1:228270483-228270533	HRE	kidney:	n/a
3	chr1:228270481-228270531	AG04450	lung:	fetal
4	chr1:228270481-228270531	Hepatocyte	liver:	n/a
5	chr1:228270483-228270533	K562	blood:	n/a
6	chr1:228270481-228270531	MCF-7	breast:	n/a
7	chr1:228270483-228270533	A549	lung:	n/a
8	chr1:228270481-228270531	HRPEpiC	eye:	n/a
9	chr1:228270481-228270531	ovcar-3	ovarian:	n/a
10	chr1:228270481-228270531	SK-N-SH	brain:	n/a
11	chr1:228270483-228270533	HIPEpiC	eye:	n/a
12	chr1:228270481-228270531	HRCEpiC	kidney:	n/a
13	chr1:228270481-228270531	Jurkat	blood:	n/a
14	chr1:228270483-228270533	AoSMC	blood vessel:	n/a
15	chr1:228270481-228270531	H1-hESC	embryonic stem cell:	embryo
16	chr1:228270481-228270531	BJ	skin:	n/a
17	chr1:228270483-228270533	GM12878	blood:	n/a
18	chr1:228270481-228270531	CMK	blood:	n/a
19	chr1:228270483-228270533	SKMC	muscle:	n/a
20	chr1:228270483-228270533	GM12892	blood:	n/a
21	chr1:228270481-228270531	HCM	heart:	n/a
22	chr1:228270481-228270531	K562	blood:	n/a
23	chr1:228270481-228270531	AG10803	skin:	n/a
24	chr1:228270481-228270531	IMR90	lung:	fetal
25	chr1:228270483-228270533	SK-N-SH_RA	brain:	n/a
26	chr1:228270483-228270533	IMR90	lung:	fetal
27	chr1:228270483-228270533	SK-N-SH	brain:	n/a
28	chr1:228270481-228270531	GM12891	blood:	n/a
29	chr1:228270483-228270533	HAEpiC	amniotic membrane:	n/a
30	chr1:228270483-228270533	HRCEpiC	kidney:	n/a
31	chr1:228270483-228270533	T-47D	breast:	n/a
32	chr1:228270483-228270533	BE2_C	brain:	n/a
33	chr1:228270481-228270531	HNPCEpiC	eye:	n/a
34	chr1:228270481-228270531	HUVEC	blood vessel:	n/a
35	chr1:228270481-228270531	HCF	heart:	n/a
36	chr1:228270481-228270531	ECC-1	luminal epithelium:	n/a
37	chr1:228270481-228270531	AoSMC	blood vessel:	n/a
38	chr1:228270481-228270531	GM12878	blood:	n/a
39	chr1:228270483-228270533	NHBE	bronchial:	n/a
40	chr1:228270481-228270531	HMEC	breast:	n/a
41	chr1:228270481-228270531	GM12892	blood:	n/a
42	chr1:228270483-228270533	AG04449	skin:	fetal
43	chr1:228270483-228270533	SAEC	small airway:	n/a
44	chr1:228270481-228270531	AG09309	skin:	n/a
45	chr1:228270483-228270533	GM06990	blood:	n/a
46	chr1:228270483-228270533	NT2-D1	testis:	n/a
47	chr1:228270483-228270533	GM19239	blood:	n/a
48	chr1:228270481-228270531	AG09319	gingival:	n/a
49	chr1:228270483-228270533	NB4	blood:	n/a
50	chr1:228270481-228270531	HEK293	kidney:	embryo

No.	Distal block	Cell Line	Cell type
1	chr1:228269915..228273320-chr1:228326449..228329096,4	K562	blood:
2	chr1:227921488..227923041-chr1:228269667..228272192,2	MCF-7	breast:
3	chr1:228268869..228271597-chr1:228699816..228701498,2	K562	blood:
4	chr1:228267816..228271023-chr1:228334433..228337364,3	K562	blood:
5	chr1:228269292..228271024-chr1:228643891..228647144,3	K562	blood:
6	chr1:228192379..228197446-chr1:228268248..228273367,9	MCF-7	breast:
7	chr1:228270227..228270808-chr1:228296563..228297459,2	NB4	blood:
8	chr1:228269794..228271921-chr1:228327972..228330804,3	MCF-7	breast:
9	chr1:45204980..45205724-chr1:228270199..228270919,2	Hela-S3	cervix:
10	chr1:228268335..228271224-chr1:228352172..228356089,4	K562	blood:
11	chr1:228268894..228271778-chr1:228351302..228354925,4	MCF-7	breast:
12	chr1:228269154..228271874-chr1:228360119..228363775,3	K562	blood:
13	chr1:228269773..228272364-chr1:228352112..228354622,6	MCF-7	breast:
14	chr1:228269306..228272326-chr1:228326148..228329488,5	MCF-7	breast:
15	chr1:228270000..228270810-chr15:75939773..75940581,2	Hela-S3	cervix:
16	chr1:227923000..227925656-chr1:228268639..228271303,2	MCF-7	breast:
17	chr1:228270338..228271968-chr1:228400103..228402238,2	MCF-7	breast:
18	chr1:228266682..228273620-chr1:228293839..228298603,9	MCF-7	breast:
19	chr1:228270141..228272243-chr1:228325927..228327960,2	MCF-7	breast:
20	chr1:228267667..228275106-chr1:228326600..228331394,10	K562	blood:
21	chr1:228270474..228272694-chr1:228336357..228338344,2	K562	blood:
22	chr1:228270437..228272083-chr1:228644163..228645827,2	MCF-7	breast:
23	chr1:228270286..228270860-chr16:88851325..88852066,2	HCT-116	colon:
24	chr1:228270277..228270944-chr16:89626682..89627322,2	Hela-S3	cervix:

Variant related genes	Relation type
ARF1	TF binding region
ARF1	CpG island
ENSG00000167526	Chromatin interaction
ENSG00000103335	Chromatin interaction
ENSG00000173548	Chromatin interaction
ENSG00000081692	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000154342	Chromatin interaction
ENSG00000143740	Chromatin interaction
ENSG00000215811	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000162913	Chromatin interaction
ENSG00000198835	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000143774	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	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
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	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
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	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
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	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
12	esv3395884	chr1:228269354-228272202	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 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	chr1:228269000-228271600	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr1:228269000-228272200	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr1:228269200-228271800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:228269200-228272000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr1:228269200-228272000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:228269200-228272200	Active TSS	Right Atrium	heart
7	chr1:228269200-228272400	Active TSS	NHLF	lung
8	chr1:228269400-228271200	Active TSS	Thymus	Thymus
9	chr1:228269400-228271400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:228269400-228271400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:228269400-228271400	Active TSS	A549	lung
12	chr1:228269400-228271400	Active TSS	GM12878-XiMat	blood
13	chr1:228269400-228271800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:228269400-228271800	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr1:228269400-228271800	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr1:228269400-228271800	Active TSS	Fetal Kidney	kidney
17	chr1:228269400-228271800	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr1:228269400-228272000	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr1:228269400-228272000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:228269400-228272000	Active TSS	NH-A	brain
21	chr1:228269400-228272400	Active TSS	HSMM	muscle
22	chr1:228269400-228272600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:228269600-228270800	Active TSS	Colonic Mucosa	Colon
24	chr1:228269600-228270800	Active TSS	HMEC	breast
25	chr1:228269600-228271000	Active TSS	Muscle Satellite Cultured Cells	--
26	chr1:228269600-228271000	Active TSS	Fetal Lung	lung
27	chr1:228269600-228271000	Active TSS	Dnd41	blood
28	chr1:228269600-228271200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:228269600-228271200	Active TSS	Primary B cells from peripheral blood	blood
30	chr1:228269600-228271200	Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr1:228269600-228271200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr1:228269600-228271200	Active TSS	Fetal Stomach	stomach
33	chr1:228269600-228271400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:228269600-228271400	Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr1:228269600-228271400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:228269600-228271400	Active TSS	Brain Cingulate Gyrus	brain
37	chr1:228269600-228271400	Active TSS	Brain Hippocampus Middle	brain
38	chr1:228269600-228271400	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr1:228269600-228271400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:228269600-228271400	Active TSS	Brain Substantia Nigra	brain
41	chr1:228269600-228271400	Active TSS	Fetal Brain Female	brain
42	chr1:228269600-228271400	Active TSS	Fetal Intestine Small	intestine
43	chr1:228269600-228271400	Active TSS	Fetal Thymus	thymus
44	chr1:228269600-228271400	Active TSS	Left Ventricle	heart
45	chr1:228269600-228271400	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr1:228269600-228271400	Active TSS	Right Ventricle	heart
47	chr1:228269600-228271400	Active TSS	K562	blood
48	chr1:228269600-228271400	Active TSS	NHEK	skin
49	chr1:228269600-228271400	Active TSS	Osteobl	bone
50	chr1:228269600-228271600	Active TSS	H1 Cell Line	embryonic stem cell

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