Variant report

Variant	rs568657003
Chromosome Location	chr12:56551659-56551660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:529)
CpG islands
(count:122)
Chromatin interactive
region (count:34)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:529 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56551094-56558885	SK-N-SH	brain:	n/a	n/a
2	REST	chr12:56551563-56551718	K562	blood:	n/a	n/a
3	SIN3AK20	chr12:56551469-56551871	A549	lung:	n/a	n/a
4	POLR2A	chr12:56551096-56559842	GM12878	blood:	n/a	n/a
5	E2F6	chr12:56551080-56552092	H1-hESC	embryonic stem cell:	n/a	chr12:56551835-56551842 chr12:56551831-56551843 chr12:56551834-56551843 chr12:56551835-56551842 chr12:56551835-56551842
6	TCF12	chr12:56550943-56553118	ECC-1	luminal epithelium:	n/a	n/a
7	ATF2	chr12:56551023-56551836	H1-hESC	embryonic stem cell:	n/a	n/a
8	ARID3A	chr12:56551510-56552276	HepG2	liver:	n/a	n/a
9	TAF1	chr12:56551527-56551822	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:56550995-56551920	GM12892	blood:	n/a	n/a
11	POLR2A	chr12:56550969-56558589	GM12892	blood:	n/a	n/a
12	CTCF	chr12:56551640-56551790	HUVEC	blood vessel:	n/a	n/a
13	FOXM1	chr12:56551391-56551866	GM12878	blood:	n/a	n/a
14	CTCF	chr12:56551465-56551855	K562	blood:	n/a	n/a
15	SPI1	chr12:56551576-56551886	GM12878	blood:	n/a	n/a
16	IRF1	chr12:56551513-56552858	K562	blood:	n/a	chr12:56552640-56552654 chr12:56552073-56552082
17	CTCF	chr12:56551616-56551793	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr12:56551620-56551770	K562	blood:	n/a	n/a
19	MYBL2	chr12:56551112-56552665	HepG2	liver:	n/a	n/a
20	POLR2A	chr12:56551250-56558611	U87	brain:	n/a	n/a
21	HDAC2	chr12:56551511-56551888	K562	blood:	n/a	n/a
22	CTCF	chr12:56551600-56551750	NHEK	skin:	n/a	n/a
23	BHLHE40	chr12:56551480-56552543	GM12878	blood:	n/a	n/a
24	MAZ	chr12:56551401-56552235	HepG2	liver:	n/a	n/a
25	TEAD4	chr12:56551310-56552549	SK-N-SH	brain:	n/a	n/a
26	MYC	chr12:56551578-56552235	MCF10A-Er-Src	breast:	n/a	n/a
27	CEBPB	chr12:56551416-56551925	A549	lung:	n/a	n/a
28	ZBTB7A	chr12:56551568-56551782	HepG2	liver:	n/a	n/a
29	FOXA1	chr12:56551443-56551857	T-47D	breast:	n/a	n/a
30	POLR2A	chr12:56551382-56551896	HUVEC	blood vessel:	n/a	n/a
31	YY1	chr12:56551341-56551888	H1-hESC	embryonic stem cell:	n/a	chr12:56551346-56551357
32	POU2F2	chr12:56551504-56552600	GM12878	blood:	n/a	chr12:56551825-56551837 chr12:56551803-56551815 chr12:56552544-56552556
33	CREB1	chr12:56551192-56552562	HepG2	liver:	n/a	chr12:56552093-56552106
34	POLR2A	chr12:56551455-56551870	HCT-116	colon:	n/a	n/a
35	CTCF	chr12:56551580-56551730	GM12872	blood:	n/a	n/a
36	CTCF	chr12:56551640-56551790	HMEC	breast:	n/a	n/a
37	CTCF	chr12:56551560-56551710	BE2_C	brain:	n/a	n/a
38	CTCF	chr12:56551600-56551750	HepG2	liver:	n/a	n/a
39	CTCF	chr12:56551591-56551794	MCF-7	breast:	n/a	n/a
40	CTCF	chr12:56551600-56551750	GM12874	blood:	n/a	n/a
41	RELA	chr12:56551106-56552534	GM15510	blood:	n/a	n/a
42	CTCF	chr12:56551640-56551790	AG09319	gingival:	n/a	n/a
43	TAF1	chr12:56551058-56552510	H1-neurons	neurons:	n/a	n/a
44	POLR2A	chr12:56551321-56551913	A549	lung:	n/a	n/a
45	SP1	chr12:56551154-56551927	H1-hESC	embryonic stem cell:	n/a	chr12:56551392-56551404 chr12:56551830-56551841 chr12:56551392-56551404 chr12:56551394-56551403 chr12:56551393-56551402 chr12:56551393-56551403 chr12:56551389-56551403
46	RAD21	chr12:56551286-56551898	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr12:56551168-56556161	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr12:56551610-56551877	A549	lung:	n/a	n/a
49	EP300	chr12:56551421-56552481	A549	lung:	n/a	n/a
50	POLR2A	chr12:56551305-56551871	K562	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:56551642-56551692	SAEC	small airway:	n/a
2	chr12:56551642-56551692	Caco-2	colon:	n/a
3	chr12:56551637-56551687	HRPEpiC	eye:	n/a
4	chr12:56551642-56551692	PFSK-1	brain:	n/a
5	chr12:56551642-56551692	GM06990	blood:	n/a
6	chr12:56551637-56551687	PrEC	prostate:	n/a
7	chr12:56551642-56551692	HCF	heart:	n/a
8	chr12:56551637-56551687	AG10803	skin:	n/a
9	chr12:56551637-56551687	HepG2	liver:	n/a
10	chr12:56551637-56551687	HCT-116	colon:	n/a
11	chr12:56551637-56551687	GM12891	blood:	n/a
12	chr12:56551637-56551687	NB4	blood:	n/a
13	chr12:56551637-56551687	AG09309	skin:	n/a
14	chr12:56551642-56551692	NH-A	brain:	n/a
15	chr12:56551637-56551687	BJ	skin:	n/a
16	chr12:56551642-56551692	ProgFib	skin:	n/a
17	chr12:56551637-56551687	GM12878	blood:	n/a
18	chr12:56551637-56551687	Hepatocyte	liver:	n/a
19	chr12:56551642-56551692	AG09319	gingival:	n/a
20	chr12:56551637-56551687	LNCaP	prostate:	n/a
21	chr12:56551637-56551687	HNPCEpiC	eye:	n/a
22	chr12:56551637-56551687	HCM	heart:	n/a
23	chr12:56551642-56551692	HUVEC	blood vessel:	n/a
24	chr12:56551642-56551692	BJ	skin:	n/a
25	chr12:56551642-56551692	AoSMC	blood vessel:	n/a
26	chr12:56551642-56551692	K562	blood:	n/a
27	chr12:56551642-56551692	HIPEpiC	eye:	n/a
28	chr12:56551637-56551687	HEK293	kidney:	embryo
29	chr12:56551642-56551692	H1-hESC	embryonic stem cell:	embryo
30	chr12:56551642-56551692	ECC-1	luminal epithelium:	n/a
31	chr12:56551637-56551687	HRCEpiC	kidney:	n/a
32	chr12:56551637-56551687	SK-N-SH	brain:	n/a
33	chr12:56551642-56551692	HNPCEpiC	eye:	n/a
34	chr12:56551642-56551692	HMEC	breast:	n/a
35	chr12:56551642-56551692	HRCEpiC	kidney:	n/a
36	chr12:56551642-56551692	HCPEpiC	choroid plexus:	n/a
37	chr12:56551637-56551687	Caco-2	colon:	n/a
38	chr12:56551642-56551692	AG09309	skin:	n/a
39	chr12:56551642-56551692	AG10803	skin:	n/a
40	chr12:56551637-56551687	HL-60	blood:	n/a
41	chr12:56551637-56551687	HAEpiC	amniotic membrane:	n/a
42	chr12:56551637-56551687	CMK	blood:	n/a
43	chr12:56551637-56551687	K562	blood:	n/a
44	chr12:56551642-56551692	A549	lung:	n/a
45	chr12:56551642-56551692	GM12891	blood:	n/a
46	chr12:56551642-56551692	SK-N-MC	brain:	n/a
47	chr12:56551642-56551692	AG04449	skin:	fetal
48	chr12:56551637-56551687	ProgFib	skin:	n/a
49	chr12:56551642-56551692	SK-N-SH_RA	brain:	n/a
50	chr12:56551637-56551687	SK-N-SH_RA	brain:	n/a

(count:34 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56550673..56553390-chr18:11908435..11911361,2	MCF-7	breast:
2	chr12:56471332..56475358-chr12:56550630..56554454,5	MCF-7	breast:
3	chr12:56434374..56437071-chr12:56550642..56553636,4	MCF-7	breast:
4	chr12:56507747..56515530-chr12:56549896..56559767,36	MCF-7	breast:
5	chr12:56551419..56552000-chr5:41870278..41870895,2	Hela-S3	cervix:
6	chr12:56434567..56436421-chr12:56551645..56554362,3	MCF-7	breast:
7	chr1:954847..956980-chr12:56550477..56552880,2	MCF-7	breast:
8	chr12:56551653..56553251-chr6:27776259..27779166,2	MCF-7	breast:
9	chr12:56551311..56554280-chr12:56613250..56616267,3	MCF-7	breast:
10	chr12:56531568..56534983-chr12:56550075..56554520,6	MCF-7	breast:
11	chr12:56480457..56482671-chr12:56551431..56553649,2	MCF-7	breast:
12	chr11:64073223..64074022-chr12:56551543..56552410,2	Hela-S3	cervix:
13	chr12:56516279..56526040-chr12:56550254..56554953,37	MCF-7	breast:
14	chr12:56549760..56554422-chr12:56650832..56654963,6	MCF-7	breast:
15	chr12:56551529..56552322-chr2:37458364..37459177,2	Hela-S3	cervix:
16	chr12:56529351..56534783-chr12:56551483..56555184,6	MCF-7	breast:
17	chr12:56550178..56557145-chr12:56575233..56584234,22	MCF-7	breast:
18	chr1:6453602..6454489-chr12:56551479..56551994,2	Hela-S3	cervix:
19	chr12:56497819..56500036-chr12:56550546..56554351,4	MCF-7	breast:
20	chr12:56551518..56552159-chr12:56582778..56583751,4	MCF-7	breast:
21	chr12:56551379..56552214-chr17:7387390..7388334,3	Hela-S3	cervix:
22	chr12:56473103..56475967-chr12:56549779..56553082,5	MCF-7	breast:
23	chr12:56551464..56551970-chr12:56582916..56583452,2	K562	blood:
24	chr12:56551520..56554242-chr12:56650975..56653538,2	MCF-7	breast:
25	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
26	chr11:62608565..62609563-chr12:56551616..56552619,4	Hela-S3	cervix:
27	chr12:56475818..56478694-chr12:56550865..56553540,2	MCF-7	breast:
28	chr12:56549752..56553222-chr12:56691115..56694737,3	K562	blood:
29	chr12:56551630..56552606-chr15:65596629..65597325,3	Hela-S3	cervix:
30	chr12:53843995..53846384-chr12:56551140..56553594,2	MCF-7	breast:
31	chr12:56549935..56553580-chr12:56615062..56619140,6	MCF-7	breast:
32	chr11:93276206..93276741-chr12:56551625..56552456,2	Hela-S3	cervix:
33	chr12:56551553..56552076-chr12:69004382..69005116,2	Hela-S3	cervix:
34	chr12:56500254..56503028-chr12:56550656..56552219,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMARCC2-2	chr12:56551418-56551729	ENSG00000257809.1

No data

Variant related genes	Relation type
MYL6	TF binding region
MYL6	CpG island
ENSG00000166002	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000197111	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000271746	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000127314	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000273141	Chromatin interaction
ENSG00000115816	Chromatin interaction
ENSG00000097021	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000173153	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000188157	Chromatin interaction
ENSG00000003509	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000154889	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000083720	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv559011	chr12:56551249-56555022	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases
3	nsv559012	chr12:56551249-56555360	Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv559013	chr12:56551249-56556389	Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv559014	chr12:56551250-56555022	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases
6	nsv559015	chr12:56551480-56555022	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56550600-56552200	Active TSS	Brain Germinal Matrix	brain
2	chr12:56550600-56552400	Active TSS	Fetal Lung	lung
3	chr12:56550600-56553000	Active TSS	GM12878-XiMat	blood
4	chr12:56550600-56553200	Active TSS	Fetal Brain Female	brain
5	chr12:56550800-56551800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr12:56550800-56551800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:56550800-56551800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:56550800-56551800	Flanking Active TSS	Fetal Muscle Leg	muscle
9	chr12:56550800-56552400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr12:56550800-56552600	Active TSS	Brain Angular Gyrus	brain
11	chr12:56550800-56552600	Active TSS	Fetal Brain Male	brain
12	chr12:56550800-56553000	Active TSS	Brain Anterior Caudate	brain
13	chr12:56550800-56553200	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr12:56550800-56553200	Active TSS	Fetal Kidney	kidney
15	chr12:56550800-56553200	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr12:56550800-56553200	Active TSS	NHDF-Ad	bronchial
17	chr12:56550800-56553400	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr12:56550800-56553400	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr12:56550800-56553400	Active TSS	Fetal Intestine Large	intestine
20	chr12:56550800-56553600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:56551000-56551800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr12:56551000-56551800	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr12:56551000-56551800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:56551000-56551800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr12:56551000-56551800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr12:56551000-56551800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:56551000-56551800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr12:56551000-56551800	Flanking Active TSS	Fetal Thymus	thymus
29	chr12:56551000-56551800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr12:56551000-56551800	Flanking Active TSS	NH-A	brain
31	chr12:56551000-56552400	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr12:56551000-56552800	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr12:56551000-56552800	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr12:56551000-56552800	Active TSS	Fetal Stomach	stomach
35	chr12:56551000-56553000	Active TSS	Brain Hippocampus Middle	brain
36	chr12:56551000-56553000	Active TSS	Brain Substantia Nigra	brain
37	chr12:56551000-56553200	Active TSS	H9 Cell Line	embryonic stem cell
38	chr12:56551000-56553200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:56551000-56553200	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr12:56551000-56553200	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr12:56551000-56553200	Active TSS	Primary T cells from cord blood	blood
42	chr12:56551000-56553200	Active TSS	Colon Smooth Muscle	Colon
43	chr12:56551000-56553200	Active TSS	Esophagus	oesophagus
44	chr12:56551000-56553200	Active TSS	Left Ventricle	heart
45	chr12:56551000-56553400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr12:56551000-56553400	Active TSS	Aorta	Aorta
47	chr12:56551000-56553400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:56551000-56553400	Active TSS	Pancreas	Pancrea
49	chr12:56551000-56553600	Active TSS	Gastric	stomach
50	chr12:56551000-56554400	Active TSS	Ovary	ovary

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