Variant report

Variant	rs56160055
Chromosome Location	chr2:30431411-30431412
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	CTCF	chr2:30431272-30431632	T-47D	breast:	n/a	chr2:30431412-30431430
2	ZNF143	chr2:30431244-30431629	GM12878	blood:	n/a	n/a
3	CTCF	chr2:30431204-30431545	ECC-1	luminal epithelium:	n/a	chr2:30431412-30431430
4	CTCF	chr2:30431360-30431510	HEEpiC	esophagus:	n/a	chr2:30431412-30431430
5	RAD21	chr2:30431237-30431809	A549	lung:	n/a	chr2:30431413-30431432
6	CTCF	chr2:30431137-30431735	A549	lung:	n/a	chr2:30431412-30431430
7	RAD21	chr2:30431223-30431756	H1-hESC	embryonic stem cell:	n/a	chr2:30431413-30431432
8	RAD21	chr2:30431200-30431646	SK-N-SH_RA	brain:	n/a	chr2:30431413-30431432
9	CTCF	chr2:30431360-30431510	HRE	kidney:	n/a	chr2:30431412-30431430
10	CTCF	chr2:30431320-30431470	GM12868	blood:	n/a	chr2:30431412-30431430
11	CTCF	chr2:30431340-30431490	GM12865	blood:	n/a	chr2:30431412-30431430
12	CTCF	chr2:30431199-30431620	K562	blood:	n/a	chr2:30431412-30431430
13	RAD21	chr2:30431135-30431870	ECC-1	luminal epithelium:	n/a	chr2:30431413-30431432
14	CTCF	chr2:30431300-30431450	GM12865	blood:	n/a	chr2:30431412-30431430
15	CTCF	chr2:30431295-30431538	Hela-S3	cervix:	n/a	chr2:30431412-30431430
16	CTCF	chr2:30431380-30431530	HepG2	liver:	n/a	chr2:30431412-30431430
17	CTCF	chr2:30431360-30431510	HCM	heart:	n/a	chr2:30431412-30431430
18	CTCF	chr2:30431205-30431628	K562	blood:	n/a	chr2:30431412-30431430
19	CTCF	chr2:30431257-30431638	HepG2	liver:	n/a	chr2:30431412-30431430
20	CTCF	chr2:30431248-30431585	Spleen_OC	spleen:	n/a	chr2:30431412-30431430
21	RAD21	chr2:30431220-30431816	Hela-S3	cervix:	n/a	chr2:30431413-30431432
22	CTCF	chr2:30431320-30431470	GM12872	blood:	n/a	chr2:30431412-30431430
23	PBX3	chr2:30431303-30431448	GM12878	blood:	n/a	n/a
24	CTCF	chr2:30431300-30431526	GM13976	blood:	n/a	chr2:30431412-30431430
25	CTCF	chr2:30431340-30431530	H1-hESC	embryonic stem cell:	n/a	chr2:30431412-30431430
26	CTCF	chr2:30431280-30431430	HCT-116	colon:	n/a	chr2:30431412-30431430
27	CTCF	chr2:30431360-30431510	SAEC	small airway:	n/a	chr2:30431412-30431430
28	CTCF	chr2:30431380-30431530	BE2_C	brain:	n/a	chr2:30431412-30431430
29	RAD21	chr2:30431163-30431776	MCF-7	breast:	n/a	chr2:30431413-30431432
30	CTCF	chr2:30431300-30431450	GM06990	blood:	n/a	chr2:30431412-30431430
31	CTCF	chr2:30431340-30431490	Caco-2	colon:	n/a	chr2:30431412-30431430
32	CTCF	chr2:30431340-30431490	AG09319	gingival:	n/a	chr2:30431412-30431430
33	TEAD4	chr2:30431301-30431629	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr2:30431209-30431653	GM12878	blood:	n/a	chr2:30431412-30431430
35	CTCF	chr2:30431294-30431600	GM19238	blood:	n/a	chr2:30431412-30431430
36	CTCF	chr2:30431340-30431490	GM12864	blood:	n/a	chr2:30431412-30431430
37	CTCF	chr2:30431300-30431450	GM12878	blood:	n/a	chr2:30431412-30431430
38	CTCF	chr2:30431400-30431550	AG04450	lung:	n/a	chr2:30431412-30431430
39	YY1	chr2:30431327-30431578	GM12878	blood:	n/a	n/a
40	CTCF	chr2:30430997-30431932	HCT-116	colon:	n/a	chr2:30431412-30431430
41	CTCF	chr2:30431340-30431490	GM06990	blood:	n/a	chr2:30431412-30431430
42	CTCF	chr2:30431340-30431490	HUVEC	blood vessel:	n/a	chr2:30431412-30431430
43	CTCF	chr2:30431340-30431490	GM12801	blood:	n/a	chr2:30431412-30431430
44	CTCF	chr2:30431048-30431666	IMR90	lung:	n/a	chr2:30431412-30431430
45	CTCF	chr2:30431260-30431520	T-47D	breast:	n/a	chr2:30431412-30431430
46	CTCF	chr2:30431320-30431470	GM12875	blood:	n/a	chr2:30431412-30431430
47	CTCF	chr2:30431380-30431530	HMEC	breast:	n/a	chr2:30431412-30431430
48	CTCF	chr2:30431340-30431490	HPAF	blood vessel:	n/a	chr2:30431412-30431430
49	CREB1	chr2:30431319-30431644	A549	lung:	n/a	n/a
50	RAD21	chr2:30431223-30431813	H1-hESC	embryonic stem cell:	n/a	chr2:30431413-30431432

No.	Distal block	Cell Line	Cell type
1	chr2:30429668..30431769-chr2:30587537..30589812,2	K562	blood:
2	chr2:30430910..30431947-chr2:30934187..30935135,9	MCF-7	breast:
3	chr2:30431314..30431957-chr2:30698160..30698830,3	MCF-7	breast:
4	chr2:30431395..30431895-chr2:30927241..30927909,2	MCF-7	breast:
5	chr2:30431081..30431711-chr2:30564436..30565032,2	MCF-7	breast:
6	chr2:30431282..30431901-chr2:30462199..30462803,2	MCF-7	breast:
7	chr2:30431012..30431788-chr2:30914178..30914838,2	MCF-7	breast:
8	chr2:30430992..30431915-chr2:30698206..30698865,2	MCF-7	breast:
9	chr2:30430979..30431952-chr2:30670002..30670748,2	K562	blood:
10	chr2:30430900..30431904-chr2:30929577..30930504,14	MCF-7	breast:
11	chr2:30431361..30432292-chr2:30934156..30935149,5	K562	blood:
12	chr2:30387528..30388513-chr2:30430980..30431915,5	MCF-7	breast:
13	chr2:30427193..30432994-chr2:30451939..30456057,6	K562	blood:
14	chr2:30430832..30432985-chr2:30454439..30456057,2	K562	blood:
15	chr2:30431027..30431865-chr2:30929589..30930554,3	MCF-7	breast:
16	chr2:30431355..30431879-chr2:30452800..30453629,3	K562	blood:
17	chr2:30429295..30431527-chr2:30928189..30930865,2	MCF-7	breast:
18	chr2:30430501..30431863-chr2:30934111..30935142,7	MCF-7	breast:
19	chr2:30430948..30431579-chr2:30929810..30930470,3	K562	blood:

Variant related genes	Relation type
ENSG00000231712	TF binding region
ENSG00000213626	Chromatin interaction
ENSG00000172954	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11690883	1.00[ASN][1000 genomes]
rs11694985	1.00[ASN][1000 genomes]
rs13030740	1.00[ASN][1000 genomes]
rs55917643	1.00[ASN][1000 genomes]
rs72785898	1.00[ASN][1000 genomes]
rs72787703	1.00[ASN][1000 genomes]
rs955214	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1002657	chr2:30339312-30516535	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv873768	chr2:30403762-30436249	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30426400-30439800	Weak transcription	Right Ventricle	heart
2	chr2:30428000-30436200	Weak transcription	Left Ventricle	heart
3	chr2:30429400-30433000	Enhancers	Fetal Thymus	thymus
4	chr2:30429800-30431600	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:30429800-30432000	Enhancers	Thymus	Thymus
6	chr2:30430400-30431600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr2:30430400-30433000	Enhancers	Fetal Heart	heart
8	chr2:30430400-30433200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr2:30430600-30431800	Enhancers	K562	blood
10	chr2:30430600-30433200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr2:30430800-30433000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:30430800-30433200	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr2:30431000-30432800	Enhancers	Primary B cells from peripheral blood	blood
14	chr2:30431000-30432800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:30431000-30433200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr2:30431200-30431800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:30431200-30432000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:30431200-30432200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:30431400-30431600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:30431400-30431600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:30431400-30431600	Enhancers	Adipose Nuclei	Adipose
22	chr2:30431400-30431800	Bivalent Enhancer	Liver	Liver
23	chr2:30431400-30431800	Enhancers	Brain Hippocampus Middle	brain
24	chr2:30431400-30431800	Enhancers	Colon Smooth Muscle	Colon
25	chr2:30431400-30431800	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr2:30431400-30431800	Enhancers	Fetal Stomach	stomach
27	chr2:30431400-30431800	Enhancers	Right Atrium	heart
28	chr2:30431400-30431800	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr2:30431400-30431800	Enhancers	Stomach Mucosa	stomach
30	chr2:30431400-30431800	Enhancers	HSMM	muscle
31	chr2:30431400-30431800	Enhancers	HSMMtube	muscle
32	chr2:30431400-30432000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr2:30431400-30432000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr2:30431400-30432000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr2:30431400-30432000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:30431400-30432000	Enhancers	Duodenum Mucosa	Duodenum
37	chr2:30431400-30432000	Enhancers	Fetal Lung	lung
38	chr2:30431400-30432000	Enhancers	Rectal Smooth Muscle	rectum
39	chr2:30431400-30432000	Enhancers	Dnd41	blood
40	chr2:30431400-30432200	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr2:30431400-30432200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr2:30431400-30432200	Enhancers	Fetal Kidney	kidney
43	chr2:30431400-30432200	Enhancers	A549	lung
44	chr2:30431400-30432400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr2:30431400-30432400	Enhancers	GM12878-XiMat	blood
46	chr2:30431400-30433000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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