Variant report

Variant	rs56057245
Chromosome Location	chr1:153539773-153539774
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	chr1:153538842-153540012	HCT-116	colon:	n/a	n/a
2	POLR2A	chr1:153538102-153539850	IMR90	lung:	n/a	n/a
3	JUND	chr1:153538750-153539796	SK-N-SH	brain:	n/a	chr1:153539206-153539216 chr1:153539205-153539217 chr1:153539169-153539178 chr1:153539207-153539215 chr1:153539208-153539219 chr1:153539167-153539178 chr1:153539206-153539216 chr1:153539206-153539216 chr1:153539205-153539216
4	NR3C1	chr1:153538836-153539935	A549	lung:	n/a	chr1:153539368-153539394 chr1:153539368-153539394 chr1:153539452-153539470 chr1:153539169-153539178 chr1:153539207-153539216
5	POLR2A	chr1:153537976-153539816	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr1:153537829-153539964	Hela-S3	cervix:	n/a	n/a
7	MAX	chr1:153538800-153539839	ECC-1	luminal epithelium:	n/a	n/a
8	FOS	chr1:153538954-153539854	MCF10A-Er-Src	breast:	n/a	chr1:153539206-153539216 chr1:153539167-153539178 chr1:153539205-153539217 chr1:153539169-153539178 chr1:153539207-153539215 chr1:153539208-153539219 chr1:153539205-153539216 chr1:153539206-153539216 chr1:153539206-153539216
9	MAX	chr1:153538792-153539814	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr1:153539561-153539904	SK-N-SH	brain:	n/a	n/a
11	MAZ	chr1:153537646-153539961	IMR90	lung:	n/a	n/a
12	SP1	chr1:153537910-153539902	A549	lung:	n/a	chr1:153539137-153539146 chr1:153539135-153539146 chr1:153539136-153539150 chr1:153539096-153539110 chr1:153539029-153539043
13	POLR2A	chr1:153537804-153539923	HCT-116	colon:	n/a	n/a
14	POLR2A	chr1:153537968-153539834	HUVEC	blood vessel:	n/a	n/a
15	TEAD4	chr1:153537703-153539867	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr1:153537764-153541614	A549	lung:	n/a	chr1:153540434-153540445
17	SP1	chr1:153537781-153539870	HCT-116	colon:	n/a	chr1:153539137-153539146 chr1:153539135-153539146 chr1:153539136-153539150 chr1:153539096-153539110 chr1:153539029-153539043
18	POLR2A	chr1:153537839-153540026	U87	brain:	n/a	n/a
19	POLR2A	chr1:153538072-153539981	Hela-S3	cervix:	n/a	n/a
20	NFIC	chr1:153538840-153539786	SK-N-SH	brain:	n/a	n/a
21	MAX	chr1:153538836-153539794	K562	blood:	n/a	n/a
22	TCF12	chr1:153537752-153541616	A549	lung:	n/a	chr1:153539098-153539108 chr1:153537891-153537901 chr1:153541146-153541156 chr1:153539241-153539251
23	POLR2A	chr1:153538781-153539873	PANC-1	pancreas:	n/a	n/a
24	NR3C1	chr1:153538811-153539924	A549	lung:	n/a	chr1:153539368-153539394 chr1:153539368-153539394 chr1:153539452-153539470 chr1:153539169-153539178 chr1:153539207-153539216
25	EP300	chr1:153538713-153539801	A549	lung:	n/a	chr1:153538969-153538979
26	POLR2A	chr1:153538027-153539907	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:153537833-153539945	U87	brain:	n/a	n/a
28	MAX	chr1:153537788-153539890	A549	lung:	n/a	n/a
29	FOSL1	chr1:153537724-153541695	HCT-116	colon:	n/a	chr1:153539206-153539216 chr1:153539205-153539217 chr1:153539169-153539178 chr1:153539207-153539215 chr1:153539208-153539219 chr1:153539206-153539216 chr1:153538365-153538374 chr1:153538361-153538372 chr1:153539206-153539216 chr1:153539205-153539216 chr1:153539167-153539178
30	SP1	chr1:153537731-153539869	HCT-116	colon:	n/a	chr1:153539137-153539146 chr1:153539135-153539146 chr1:153539136-153539150 chr1:153539096-153539110 chr1:153539029-153539043
31	TCF12	chr1:153537730-153539946	SK-N-SH	brain:	n/a	chr1:153539098-153539108 chr1:153537891-153537901 chr1:153539241-153539251
32	JUND	chr1:153537810-153539795	SK-N-SH	brain:	n/a	chr1:153539206-153539216 chr1:153539205-153539217 chr1:153539169-153539178 chr1:153539207-153539215 chr1:153539208-153539219 chr1:153539167-153539178 chr1:153539206-153539216 chr1:153538365-153538374 chr1:153538361-153538372 chr1:153539206-153539216 chr1:153539205-153539216
33	RCOR1	chr1:153537929-153539878	IMR90	lung:	n/a	n/a
34	POLR2A	chr1:153538625-153539885	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr1:153537876-153539810	Hela-S3	cervix:	n/a	n/a
36	REST	chr1:153538747-153539823	A549	lung:	n/a	n/a
37	POLR2A	chr1:153538807-153539778	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr1:153539742-153539858	A549	lung:	n/a	n/a
39	GATA3	chr1:153537960-153539823	A549	lung:	n/a	chr1:153538363-153538372
40	FOSL2	chr1:153537800-153539862	A549	lung:	n/a	chr1:153539206-153539216 chr1:153539205-153539217 chr1:153539169-153539178 chr1:153539207-153539215 chr1:153539208-153539219 chr1:153539206-153539216 chr1:153538365-153538374 chr1:153538361-153538372 chr1:153539206-153539216 chr1:153539168-153539179
41	POLR2A	chr1:153538108-153540254	PANC-1	pancreas:	n/a	n/a
42	YY1	chr1:153538796-153539795	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153538054..153540599-chr1:153598556..153600339,3	K562	blood:
2	chr1:153535304..153546939-chr1:153598248..153612195,40	MCF-7	breast:
3	chr1:153537679..153540436-chr1:153962275..153964884,2	K562	blood:
4	chr1:153504456..153510099-chr1:153538941..153542898,8	K562	blood:
5	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
6	chr1:153515310..153522123-chr1:153537390..153541283,13	MCF-7	breast:
7	chr1:153537973..153540755-chr1:153602282..153604926,2	K562	blood:
8	chr1:153539289..153541606-chr1:153604560..153606747,2	K562	blood:
9	chr1:153517686..153519228-chr1:153538736..153541189,3	K562	blood:
10	chr1:153516187..153518294-chr1:153538747..153540345,2	K562	blood:
11	chr1:153539321..153541162-chr1:153580987..153583409,2	K562	blood:
12	chr1:153514173..153516527-chr1:153537925..153539864,2	K562	blood:
13	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
14	chr1:153539127..153551919-chr1:153598146..153608314,34	MCF-7	breast:
15	chr1:153503567..153510701-chr1:153536906..153541884,20	MCF-7	breast:
16	chr1:153522267..153525133-chr1:153537337..153540137,3	MCF-7	breast:
17	chr1:153534464..153536760-chr1:153538176..153540228,3	MCF-7	breast:
18	chr1:153536449..153542914-chr1:153579157..153590800,34	MCF-7	breast:
19	chr1:153504897..153511307-chr1:153536318..153542519,37	MCF-7	breast:
20	chr1:153537683..153540046-chr1:153895076..153896651,2	K562	blood:
21	chr1:153327681..153330764-chr1:153538971..153541656,5	MCF-7	breast:
22	chr1:153536608..153541746-chr1:153698648..153702694,5	MCF-7	breast:
23	chr1:153537634..153542525-chr1:153598837..153602183,9	K562	blood:

Variant related genes	Relation type
S100A2	TF binding region
ENSG00000163220	Chromatin interaction
ENSG00000188015	Chromatin interaction
ENSG00000196420	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000199565	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000143614	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000160678	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1047325	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050923	0.84[EUR][1000 genomes]
rs11488669	0.82[EUR][1000 genomes]
rs16835437	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16835455	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28452456	0.84[EUR][1000 genomes]
rs28548347	0.84[EUR][1000 genomes]
rs28594230	0.82[EUR][1000 genomes]
rs28689606	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718953	0.84[EUR][1000 genomes]
rs36022742	0.84[EUR][1000 genomes]
rs3762268	0.84[EUR][1000 genomes]
rs41265162	0.84[EUR][1000 genomes]
rs41265164	0.84[EUR][1000 genomes]
rs4595398	0.84[EUR][1000 genomes]
rs55955983	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56043239	0.84[EUR][1000 genomes]
rs56089062	0.84[EUR][1000 genomes]
rs56350425	0.84[EUR][1000 genomes]
rs56838169	0.84[EUR][1000 genomes]
rs57024596	0.84[EUR][1000 genomes]
rs58056804	0.87[EUR][1000 genomes]
rs58072118	0.84[EUR][1000 genomes]
rs59376279	0.84[EUR][1000 genomes]
rs60069797	1.00[ASN][1000 genomes]
rs60218214	0.84[EUR][1000 genomes]
rs60287468	0.87[EUR][1000 genomes]
rs61265945	0.84[EUR][1000 genomes]
rs61558997	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427301	0.84[EUR][1000 genomes]
rs6671398	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700310	0.82[EUR][1000 genomes]
rs6702891	1.00[ASN][1000 genomes]
rs6703014	1.00[ASN][1000 genomes]
rs73026350	0.84[EUR][1000 genomes]
rs74115473	0.87[EUR][1000 genomes]
rs74115476	0.81[EUR][1000 genomes]
rs8401	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
4	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153535800-153540800	Enhancers	Fetal Muscle Leg	muscle
2	chr1:153535800-153541600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:153536000-153540800	Enhancers	Fetal Muscle Trunk	muscle
4	chr1:153536000-153541600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:153536000-153541600	Enhancers	Placenta	Placenta
6	chr1:153536000-153541600	Enhancers	Lung	lung
7	chr1:153536000-153542000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:153536200-153541800	Enhancers	Placenta Amnion	Placenta Amnion
9	chr1:153536600-153541000	Enhancers	Fetal Intestine Large	intestine
10	chr1:153536800-153540800	Enhancers	Stomach Mucosa	stomach
11	chr1:153536800-153541800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:153537000-153540800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr1:153537000-153541600	Enhancers	HUVEC	blood vessel
14	chr1:153537600-153541600	Enhancers	Primary hematopoietic stem cells	blood
15	chr1:153537800-153539800	Enhancers	Primary B cells from peripheral blood	blood
16	chr1:153537800-153539800	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr1:153537800-153539800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr1:153537800-153539800	Enhancers	GM12878-XiMat	blood
19	chr1:153537800-153540000	Enhancers	Fetal Lung	lung
20	chr1:153537800-153540400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr1:153537800-153540400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr1:153537800-153540400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:153537800-153540400	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr1:153537800-153540600	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr1:153537800-153540600	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr1:153537800-153540800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr1:153537800-153540800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr1:153537800-153540800	Enhancers	Right Ventricle	heart
29	chr1:153537800-153540800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr1:153537800-153541000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:153537800-153541000	Enhancers	Primary B cells from cord blood	blood
32	chr1:153537800-153541600	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr1:153537800-153541600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:153537800-153541600	Enhancers	Fetal Heart	heart
35	chr1:153537800-153541600	Enhancers	Fetal Thymus	thymus
36	chr1:153537800-153541800	Flanking Active TSS	Hela-S3	cervix
37	chr1:153538000-153539800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr1:153538000-153539800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr1:153538000-153539800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:153538000-153539800	Flanking Active TSS	HMEC	breast
41	chr1:153538000-153540000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:153538000-153540400	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr1:153538000-153540800	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr1:153538000-153540800	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr1:153538000-153540800	Enhancers	Fetal Kidney	kidney
46	chr1:153538000-153541000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:153538000-153541000	Enhancers	Right Atrium	heart
48	chr1:153538000-153541200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:153538000-153541200	Enhancers	Psoas Muscle	Psoas
50	chr1:153538000-153541400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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