Variant report

Variant	rs535285775
Chromosome Location	chr13:52026709-52026710
allele	A/G
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	chr13:52026419-52027407	GM12878	blood:	n/a	n/a
2	POLR2A	chr13:52026443-52028489	GM12892	blood:	n/a	n/a
3	POLR2A	chr13:52025546-52028013	HCT-116	colon:	n/a	n/a
4	YY1	chr13:52026680-52028032	HepG2	liver:	n/a	chr13:52027680-52027691 chr13:52027209-52027220
5	TAF1	chr13:52026482-52027889	ECC-1	luminal epithelium:	n/a	n/a
6	MAX	chr13:52026576-52028300	Hela-S3	cervix:	n/a	chr13:52027243-52027256 chr13:52027244-52027255 chr13:52027245-52027254 chr13:52027244-52027255 chr13:52027240-52027259
7	TAF7	chr13:52026410-52027370	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr13:52026620-52026770	AG09319	gingival:	n/a	n/a
9	POU2F2	chr13:52026559-52027322	GM12878	blood:	n/a	chr13:52027294-52027305 chr13:52027295-52027303 chr13:52027290-52027308 chr13:52027288-52027310 chr13:52027292-52027304 chr13:52027296-52027309 chr13:52027296-52027309 chr13:52027294-52027304 chr13:52027291-52027306
10	HEY1	chr13:52026487-52028443	HepG2	liver:	n/a	chr13:52028218-52028227
11	POLR2A	chr13:52026068-52028050	HCT-116	colon:	n/a	n/a
12	TAL1	chr13:52025280-52027330	K562	blood:	n/a	n/a
13	POLR2A	chr13:52025630-52028095	HEK293	kidney:	n/a	n/a
14	POLR2A	chr13:52023042-52028956	GM12878	blood:	n/a	n/a
15	CHD1	chr13:52024742-52028646	IMR90	lung:	n/a	n/a
16	SIN3AK20	chr13:52026114-52026833	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr13:52026482-52026812	H1-neurons	neurons:	n/a	n/a
18	CREB1	chr13:52026504-52028397	GM12878	blood:	n/a	n/a
19	CHD1	chr13:52025386-52028410	GM12878	blood:	n/a	n/a
20	CCNT2	chr13:52025623-52028030	K562	blood:	n/a	chr13:52027316-52027325 chr13:52025953-52025962 chr13:52027432-52027441
21	CREB1	chr13:52026517-52028100	HepG2	liver:	n/a	n/a
22	POLR2A	chr13:52025562-52028409	H1-neurons	neurons:	n/a	n/a
23	CTCF	chr13:52026620-52026770	AG04449	skin:	n/a	n/a
24	NFATC1	chr13:52026507-52027373	GM12878	blood:	n/a	n/a
25	SMARCB1	chr13:52026054-52028371	Hela-S3	cervix:	n/a	n/a
26	TAF1	chr13:52026481-52027959	H1-hESC	embryonic stem cell:	n/a	n/a
27	EP300	chr13:52026587-52028344	GM12878	blood:	n/a	chr13:52027717-52027726 chr13:52028128-52028138 chr13:52027688-52027704 chr13:52027595-52027611
28	POLR2A	chr13:52025258-52028416	K562	blood:	n/a	n/a
29	SP1	chr13:52026661-52028042	GM12878	blood:	n/a	chr13:52027432-52027442 chr13:52027431-52027443 chr13:52027221-52027230 chr13:52027428-52027442 chr13:52027431-52027443 chr13:52027368-52027380 chr13:52027433-52027442 chr13:52027370-52027379 chr13:52027432-52027441 chr13:52027433-52027442 chr13:52027316-52027325 chr13:52027220-52027232 chr13:52027579-52027586 chr13:52027528-52027549 chr13:52027220-52027232 chr13:52027432-52027442 chr13:52027317-52027326
30	BCLAF1	chr13:52026022-52028384	GM12878	blood:	n/a	chr13:52027205-52027218 chr13:52027799-52027808 chr13:52027221-52027230 chr13:52027312-52027325 chr13:52027317-52027326 chr13:52027680-52027693
31	TAF1	chr13:52026045-52026744	K562	blood:	n/a	n/a
32	STAT1	chr13:52026225-52028498	GM12878	blood:	n/a	chr13:52028254-52028262
33	POLR2A	chr13:52025371-52028505	GM18951	blood:	n/a	n/a
34	REST	chr13:52025376-52028611	H1-neurons	neurons:	n/a	chr13:52027338-52027356 chr13:52025635-52025644 chr13:52025993-52026006
35	POLR2A	chr13:52025569-52028397	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr13:52025590-52028395	MCF-7	breast:	n/a	n/a
37	POLR2A	chr13:52026449-52027443	SK-N-MC	brain:	n/a	n/a
38	POLR2A	chr13:52025428-52028620	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr13:52024109-52028486	GM18505	blood:	n/a	n/a
40	POLR2A	chr13:52026465-52027313	A549	lung:	n/a	n/a
41	POLR2A	chr13:52025660-52028535	H1-hESC	embryonic stem cell:	n/a	n/a
42	ETS1	chr13:52026664-52027317	GM12878	blood:	n/a	n/a
43	POLR2A	chr13:52023653-52028418	HepG2	liver:	n/a	n/a
44	POLR2A	chr13:52026493-52027923	U87	brain:	n/a	n/a
45	EP300	chr13:52026705-52026768	GM12878	blood:	n/a	n/a
46	POLR2A	chr13:52025620-52028387	K562	blood:	n/a	n/a
47	POLR2A	chr13:52025901-52028516	GM12891	blood:	n/a	n/a
48	MTA3	chr13:52025208-52028795	GM12878	blood:	n/a	n/a
49	CTCF	chr13:52026640-52026790	HMEC	breast:	n/a	n/a
50	POLR2A	chr13:52025507-52028083	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:149858264..149859990-chr13:52025489..52027316,2	MCF-7	breast:
2	chr13:52025774..52028487-chr13:52584807..52587141,2	K562	blood:
3	chr13:52026651..52027516-chr13:77566146..77566803,2	NB4	blood:
4	chr13:52022728..52028464-chr13:52376436..52381467,17	K562	blood:
5	chr13:52023047..52029598-chr13:52376243..52380914,21	K562	blood:
6	chr13:52022475..52029228-chr13:52156654..52162250,29	K562	blood:
7	chr13:52026493..52027134-chr19:59029953..59030938,2	NB4	blood:
8	chr13:51933288..51938259-chr13:52024808..52026901,4	K562	blood:
9	chr13:52026671..52027516-chr6:27100678..27101257,2	NB4	blood:
10	chr13:52026056..52028727-chr13:52040719..52045413,5	K562	blood:
11	chr13:51995533..51997582-chr13:52026152..52028042,2	K562	blood:
12	chr13:52025793..52028352-chr13:52043580..52045211,2	MCF-7	breast:
13	chr13:52026582..52027992-chr13:52157336..52159523,9	MCF-7	breast:
14	chr13:52026611..52027282-chr13:111367415..111368502,3	Hela-S3	cervix:
15	chr13:51996691..52002238-chr13:52025569..52028541,7	MCF-7	breast:
16	chr11:71823458..71824149-chr13:52026625..52027625,2	NB4	blood:
17	chr13:52025794..52034237-chr13:52040132..52048046,20	K562	blood:
18	chr13:52025248..52027565-chr13:52113097..52117557,5	K562	blood:
19	chr13:52025577..52029967-chr13:52343918..52348772,7	MCF-7	breast:
20	chr13:52024953..52028665-chr13:52311565..52316008,5	MCF-7	breast:
21	chr11:62340893..62341654-chr13:52026705..52027451,2	NB4	blood:
22	chr13:52025241..52027687-chr13:52171016..52174536,3	MCF-7	breast:
23	chr13:52026302..52028472-chr13:52069042..52071707,2	MCF-7	breast:
24	chr13:52024267..52031024-chr13:52038927..52044194,9	MCF-7	breast:
25	chr13:52024232..52029374-chr13:52366504..52381003,28	MCF-7	breast:
26	chr13:52026585..52027571-chr7:139043748..139044634,2	NB4	blood:
27	chr11:95523018..95523520-chr13:52026610..52027555,2	NB4	blood:
28	chr13:52022285..52029211-chr13:52148229..52167071,88	MCF-7	breast:
29	chr13:52026703..52027221-chr7:140097973..140098689,2	HCT-116	colon:
30	chr13:52026520..52027249-chr13:52158446..52159271,2	NB4	blood:
31	chr13:51994030..51996463-chr13:52024763..52027853,3	MCF-7	breast:
32	chr12:104234703..104235400-chr13:52026637..52027270,2	Hela-S3	cervix:
33	chr13:52025027..52027980-chr2:128047526..128049328,2	MCF-7	breast:
34	chr13:52024284..52029908-chr13:52069886..52073128,6	K562	blood:
35	chr13:51959134..51961591-chr13:52026035..52028339,2	K562	blood:
36	chr13:52024964..52027210-chr3:57581929..57583601,2	MCF-7	breast:
37	chr13:52025248..52026911-chr13:52113097..52115719,3	K562	blood:
38	chr13:52025709..52029684-chr13:52361886..52365561,3	MCF-7	breast:
39	chr13:52025134..52027888-chr13:53029090..53030597,2	MCF-7	breast:
40	chr11:62609151..62609696-chr13:52026692..52027236,2	NB4	blood:
41	chr12:27175144..27175751-chr13:52026590..52027135,2	NB4	blood:
42	chr13:52022042..52032158-chr13:52153162..52160287,46	K562	blood:
43	chr1:935164..937657-chr13:52026309..52028447,2	MCF-7	breast:
44	chr13:52022276..52028052-chr13:52350866..52359408,15	MCF-7	breast:
45	chr13:52026132..52027003-chr15:60770557..60771410,2	NB4	blood:
46	chr13:52024743..52028940-chr13:52112359..52118516,11	MCF-7	breast:
47	chr13:52026651..52027187-chr14:81686972..81687730,2	NB4	blood:
48	chr13:52026692..52027349-chr9:4984498..4985175,2	HCT-116	colon:
49	chr13:52025316..52028305-chr18:3447499..3449683,2	MCF-7	breast:
50	chr13:52026564..52027860-chr13:52157626..52159049,8	MCF-7	breast:

Variant related genes	Relation type
RPS4XP16	TF binding region
INTS6-AS1	TF binding region
INTS6	TF binding region
ENSG00000152944	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000177426	Chromatin interaction
ENSG00000224451	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000157800	Chromatin interaction
ENSG00000096968	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000252141	Chromatin interaction
ENSG00000231856	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000110200	Chromatin interaction
ENSG00000229906	Chromatin interaction
ENSG00000273391	Chromatin interaction
ENSG00000168439	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000168374	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000243900	Chromatin interaction
ENSG00000270101	Chromatin interaction
ENSG00000166037	Chromatin interaction
ENSG00000165417	Chromatin interaction
ENSG00000146963	Chromatin interaction
ENSG00000123191	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000102796	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000128915	Chromatin interaction
ENSG00000188290	Chromatin interaction
ENSG00000253710	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000136108	Chromatin interaction
ENSG00000139668	Chromatin interaction
ENSG00000119574	Chromatin interaction
ENSG00000163161	Chromatin interaction
ENSG00000272146	Chromatin interaction
ENSG00000245534	Chromatin interaction
ENSG00000257327	Chromatin interaction
ENSG00000206920	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000102805	Chromatin interaction
ENSG00000269965	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3421830	chr13:52024776-52027324	Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	esv3360115	chr13:52025676-52027974	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 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	chr13:52024400-52028200	Active TSS	Thymus	Thymus
2	chr13:52024800-52027200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr13:52025000-52028000	Active TSS	Hela-S3	cervix
4	chr13:52025000-52028000	Active TSS	HMEC	breast
5	chr13:52025000-52028200	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr13:52025000-52028200	Active TSS	Primary T cells fromperipheralblood	blood
7	chr13:52025000-52028200	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr13:52025000-52028600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr13:52025000-52028600	Active TSS	Right Ventricle	heart
10	chr13:52025000-52028800	Active TSS	Fetal Muscle Leg	muscle
11	chr13:52025000-52028800	Active TSS	K562	blood
12	chr13:52025000-52029000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr13:52025000-52029000	Active TSS	GM12878-XiMat	blood
14	chr13:52025200-52027200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr13:52025200-52028000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr13:52025200-52028000	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr13:52025200-52028000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr13:52025200-52028000	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr13:52025200-52028000	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr13:52025200-52028000	Active TSS	NHLF	lung
21	chr13:52025200-52028200	Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr13:52025200-52028200	Active TSS	Brain Cingulate Gyrus	brain
23	chr13:52025200-52028200	Active TSS	Stomach Smooth Muscle	stomach
24	chr13:52025200-52028200	Active TSS	HSMMtube	muscle
25	chr13:52025200-52028400	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr13:52025200-52028600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr13:52025200-52028600	Active TSS	H1 Cell Line	embryonic stem cell
28	chr13:52025200-52028600	Active TSS	H9 Cell Line	embryonic stem cell
29	chr13:52025200-52028600	Active TSS	Aorta	Aorta
30	chr13:52025200-52028600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr13:52025200-52028600	Active TSS	Fetal Muscle Trunk	muscle
32	chr13:52025200-52028600	Active TSS	Lung	lung
33	chr13:52025200-52028600	Active TSS	A549	lung
34	chr13:52025200-52028800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr13:52025200-52028800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr13:52025200-52028800	Active TSS	Fetal Intestine Small	intestine
37	chr13:52025200-52028800	Active TSS	Fetal Thymus	thymus
38	chr13:52025200-52028800	Active TSS	Psoas Muscle	Psoas
39	chr13:52025200-52028800	Active TSS	NHDF-Ad	bronchial
40	chr13:52025400-52027800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr13:52025400-52028000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr13:52025400-52028000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr13:52025400-52028000	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr13:52025400-52028000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr13:52025400-52028200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr13:52025400-52028200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr13:52025400-52028200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr13:52025400-52028200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr13:52025400-52028200	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr13:52025400-52028200	Active TSS	Brain Hippocampus Middle	brain

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