Variant report

Variant	rs542292934
Chromosome Location	chr12:56551920-56551921
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:322)
CpG islands
(count:0)
Chromatin interactive
region (count:49)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:322 , 50 per page) page: 1 2 3 4 5 6 7

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	POLR2A	chr12:56551096-56559842	GM12878	blood:	n/a	n/a
3	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
4	TCF12	chr12:56550943-56553118	ECC-1	luminal epithelium:	n/a	n/a
5	JUND	chr12:56551902-56552308	H1-hESC	embryonic stem cell:	n/a	chr12:56552095-56552104
6	POLR2A	chr12:56551899-56559978	HUVEC	blood vessel:	n/a	n/a
7	ARID3A	chr12:56551510-56552276	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:56550995-56551920	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:56550969-56558589	GM12892	blood:	n/a	n/a
10	REST	chr12:56551917-56552376	K562	blood:	n/a	n/a
11	POLR2A	chr12:56551911-56556101	SK-N-SH	brain:	n/a	n/a
12	IRF1	chr12:56551513-56552858	K562	blood:	n/a	chr12:56552640-56552654 chr12:56552073-56552082
13	MYBL2	chr12:56551112-56552665	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:56551250-56558611	U87	brain:	n/a	n/a
15	CTCF	chr12:56551920-56552070	AG10803	skin:	n/a	n/a
16	BHLHE40	chr12:56551480-56552543	GM12878	blood:	n/a	n/a
17	MAZ	chr12:56551401-56552235	HepG2	liver:	n/a	n/a
18	CEBPD	chr12:56551920-56553357	K562	blood:	n/a	n/a
19	TEAD4	chr12:56551310-56552549	SK-N-SH	brain:	n/a	n/a
20	MYC	chr12:56551578-56552235	MCF10A-Er-Src	breast:	n/a	n/a
21	CEBPB	chr12:56551416-56551925	A549	lung:	n/a	n/a
22	POU2F2	chr12:56551504-56552600	GM12878	blood:	n/a	chr12:56551825-56551837 chr12:56551803-56551815 chr12:56552544-56552556
23	CREB1	chr12:56551192-56552562	HepG2	liver:	n/a	chr12:56552093-56552106
24	JUND	chr12:56551919-56552542	SK-N-SH	brain:	n/a	chr12:56552095-56552104
25	RELA	chr12:56551106-56552534	GM15510	blood:	n/a	n/a
26	TAF1	chr12:56551058-56552510	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr12:56551826-56552491	A549	lung:	n/a	n/a
28	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
29	POLR2A	chr12:56551168-56556161	H1-hESC	embryonic stem cell:	n/a	n/a
30	EP300	chr12:56551421-56552481	A549	lung:	n/a	n/a
31	RFX5	chr12:56551275-56552357	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr12:56551896-56556539	HCT-116	colon:	n/a	n/a
33	CTCF	chr12:56551055-56552716	A549	lung:	n/a	n/a
34	POLR2A	chr12:56551408-56556564	K562	blood:	n/a	n/a
35	MAX	chr12:56551191-56552570	GM12878	blood:	n/a	chr12:56551393-56551403
36	MAX	chr12:56551151-56552220	SK-N-SH	brain:	n/a	chr12:56551393-56551403
37	POLR2A	chr12:56550856-56557007	HepG2	liver:	n/a	n/a
38	POU2F2	chr12:56551901-56552635	GM12891	blood:	n/a	chr12:56552544-56552556
39	CTCF	chr12:56551529-56552129	K562	blood:	n/a	n/a
40	YY1	chr12:56551907-56552582	H1-hESC	embryonic stem cell:	n/a	chr12:56552181-56552193 chr12:56552175-56552195
41	EP300	chr12:56551901-56552351	T-47D	breast:	n/a	n/a
42	RFX5	chr12:56551913-56552350	GM12878	blood:	n/a	n/a
43	POLR2A	chr12:56551816-56553252	HepG2	liver:	n/a	n/a
44	ZKSCAN1	chr12:56551537-56552370	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr12:56551369-56560498	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr12:56551498-56553336	HepG2	liver:	n/a	n/a
47	JUN	chr12:56551910-56552291	HepG2	liver:	n/a	chr12:56552095-56552104 chr12:56552091-56552104
48	POLR2A	chr12:56551123-56558578	Hela-S3	cervix:	n/a	n/a
49	TBP	chr12:56551246-56553360	H1-hESC	embryonic stem cell:	n/a	n/a
50	GTF2B	chr12:56551436-56552564	K562	blood:	n/a	n/a

No data

(count:49 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56551774..56552533-chr7:5569851..5571111,3	Hela-S3	cervix:
2	chr12:56550673..56553390-chr18:11908435..11911361,2	MCF-7	breast:
3	chr12:56471332..56475358-chr12:56550630..56554454,5	MCF-7	breast:
4	chr12:56434374..56437071-chr12:56550642..56553636,4	MCF-7	breast:
5	chr12:56551919..56552646-chr2:99797563..99798171,2	Hela-S3	cervix:
6	chr12:56507747..56515530-chr12:56549896..56559767,36	MCF-7	breast:
7	chr12:56209755..56212447-chr12:56551879..56553739,2	MCF-7	breast:
8	chr12:56551784..56552504-chr2:25194556..25195403,2	Hela-S3	cervix:
9	chr12:56551814..56552599-chr5:130506602..130507176,2	NB4	blood:
10	chr12:56551419..56552000-chr5:41870278..41870895,2	Hela-S3	cervix:
11	chr12:56434567..56436421-chr12:56551645..56554362,3	MCF-7	breast:
12	chr1:954847..956980-chr12:56550477..56552880,2	MCF-7	breast:
13	chr12:56551653..56553251-chr6:27776259..27779166,2	MCF-7	breast:
14	chr12:56551311..56554280-chr12:56613250..56616267,3	MCF-7	breast:
15	chr12:56531568..56534983-chr12:56550075..56554520,6	MCF-7	breast:
16	chr12:56480457..56482671-chr12:56551431..56553649,2	MCF-7	breast:
17	chr11:64073223..64074022-chr12:56551543..56552410,2	Hela-S3	cervix:
18	chr12:56516279..56526040-chr12:56550254..56554953,37	MCF-7	breast:
19	chr12:56549760..56554422-chr12:56650832..56654963,6	MCF-7	breast:
20	chr12:56434092..56435829-chr12:56551661..56553282,2	K562	blood:
21	chr12:56551838..56552458-chr7:21984929..21985891,2	HCT-116	colon:
22	chr12:56551529..56552322-chr2:37458364..37459177,2	Hela-S3	cervix:
23	chr1:100503008..100503955-chr12:56551709..56552540,2	Hela-S3	cervix:
24	chr12:56529351..56534783-chr12:56551483..56555184,6	MCF-7	breast:
25	chr12:56550178..56557145-chr12:56575233..56584234,22	MCF-7	breast:
26	chr1:6453602..6454489-chr12:56551479..56551994,2	Hela-S3	cervix:
27	chr12:56497819..56500036-chr12:56550546..56554351,4	MCF-7	breast:
28	chr12:56551518..56552159-chr12:56582778..56583751,4	MCF-7	breast:
29	chr12:56551379..56552214-chr17:7387390..7388334,3	Hela-S3	cervix:
30	chr12:56473103..56475967-chr12:56549779..56553082,5	MCF-7	breast:
31	chr12:56551464..56551970-chr12:56582916..56583452,2	K562	blood:
32	chr12:56551520..56554242-chr12:56650975..56653538,2	MCF-7	breast:
33	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
34	chr11:62608565..62609563-chr12:56551616..56552619,4	Hela-S3	cervix:
35	chr12:56475818..56478694-chr12:56550865..56553540,2	MCF-7	breast:
36	chr12:56551685..56552542-chr17:56708452..56709440,2	HCT-116	colon:
37	chr12:56549752..56553222-chr12:56691115..56694737,3	K562	blood:
38	chr12:56551630..56552606-chr15:65596629..65597325,3	Hela-S3	cervix:
39	chr12:56551805..56552522-chr13:77600819..77601817,2	Hela-S3	cervix:
40	chr12:53843995..53846384-chr12:56551140..56553594,2	MCF-7	breast:
41	chr12:56551730..56554656-chr12:57027945..57032236,3	K562	blood:
42	chr12:56551913..56552508-chr7:39988805..39989416,2	Hela-S3	cervix:
43	chr12:56551727..56552536-chr6:13574659..13575232,2	Hela-S3	cervix:
44	chr12:56551787..56553694-chr12:56657880..56660758,2	MCF-7	breast:
45	chr1:155531963..155532590-chr12:56551850..56552623,2	Hela-S3	cervix:
46	chr12:56549935..56553580-chr12:56615062..56619140,6	MCF-7	breast:
47	chr11:93276206..93276741-chr12:56551625..56552456,2	Hela-S3	cervix:
48	chr12:56551553..56552076-chr12:69004382..69005116,2	Hela-S3	cervix:
49	chr12:56500254..56503028-chr12:56550656..56552219,2	MCF-7	breast:

No data

Variant related genes	Relation type
MYL6	TF binding region
ENSG00000197728	Chromatin interaction
ENSG00000164649	Chromatin interaction
ENSG00000115816	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000005812	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000116539	Chromatin interaction
ENSG00000173153	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000166002	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000124523	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000115137	Chromatin interaction
ENSG00000083720	Chromatin interaction
ENSG00000097021	Chromatin interaction
ENSG00000273141	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000154889	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000003509	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000188157	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000156875	Chromatin interaction
ENSG00000186687	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000224165	Chromatin interaction
ENSG00000271746	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000197111	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000241962	Chromatin interaction
ENSG00000185414	Chromatin interaction
ENSG00000075624	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000127314	Chromatin interaction
ENSG00000259826	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000135482	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	chr12:56550800-56552400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr12:56550800-56552600	Active TSS	Brain Angular Gyrus	brain
7	chr12:56550800-56552600	Active TSS	Fetal Brain Male	brain
8	chr12:56550800-56553000	Active TSS	Brain Anterior Caudate	brain
9	chr12:56550800-56553200	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr12:56550800-56553200	Active TSS	Fetal Kidney	kidney
11	chr12:56550800-56553200	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr12:56550800-56553200	Active TSS	NHDF-Ad	bronchial
13	chr12:56550800-56553400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr12:56550800-56553400	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr12:56550800-56553400	Active TSS	Fetal Intestine Large	intestine
16	chr12:56550800-56553600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:56551000-56552400	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr12:56551000-56552800	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr12:56551000-56552800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr12:56551000-56552800	Active TSS	Fetal Stomach	stomach
21	chr12:56551000-56553000	Active TSS	Brain Hippocampus Middle	brain
22	chr12:56551000-56553000	Active TSS	Brain Substantia Nigra	brain
23	chr12:56551000-56553200	Active TSS	H9 Cell Line	embryonic stem cell
24	chr12:56551000-56553200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:56551000-56553200	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr12:56551000-56553200	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr12:56551000-56553200	Active TSS	Primary T cells from cord blood	blood
28	chr12:56551000-56553200	Active TSS	Colon Smooth Muscle	Colon
29	chr12:56551000-56553200	Active TSS	Esophagus	oesophagus
30	chr12:56551000-56553200	Active TSS	Left Ventricle	heart
31	chr12:56551000-56553400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:56551000-56553400	Active TSS	Aorta	Aorta
33	chr12:56551000-56553400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:56551000-56553400	Active TSS	Pancreas	Pancrea
35	chr12:56551000-56553600	Active TSS	Gastric	stomach
36	chr12:56551000-56554400	Active TSS	Ovary	ovary
37	chr12:56551200-56552600	Active TSS	A549	lung
38	chr12:56551200-56553200	Active TSS	H1 Cell Line	embryonic stem cell
39	chr12:56551200-56553400	Active TSS	Psoas Muscle	Psoas
40	chr12:56551200-56553400	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr12:56551200-56554200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr12:56551400-56552400	Active TSS	Primary B cells from peripheral blood	blood
43	chr12:56551400-56552400	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr12:56551400-56552600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr12:56551400-56552600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:56551400-56552800	Active TSS	Primary monocytes fromperipheralblood	blood
47	chr12:56551400-56552800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr12:56551400-56552800	Active TSS	Thymus	Thymus
49	chr12:56551400-56553000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:56551400-56553000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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