Variant report

Variant	rs535470004
Chromosome Location	chr12:49453557-49453558
allele	A/C/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	POLR2A	chr12:49453535-49455032	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD1	chr12:49451619-49455170	IMR90	lung:	n/a	chr12:49454043-49454053 chr12:49454374-49454384 chr12:49453842-49453852
3	POLR2A	chr12:49452782-49455199	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr12:49453533-49455168	HUVEC	blood vessel:	n/a	n/a
5	UBTF	chr12:49452969-49454790	K562	blood:	n/a	n/a
6	TCF12	chr12:49452603-49453813	A549	lung:	n/a	n/a
7	MAX	chr12:49453436-49455228	ECC-1	luminal epithelium:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49453616-49453625 chr12:49454690-49454701
8	POLR2A	chr12:49453033-49455284	Hela-S3	cervix:	n/a	n/a
9	MTA3	chr12:49452741-49455410	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:49453336-49455117	GM18951	blood:	n/a	n/a
11	ZBTB7A	chr12:49453334-49453624	K562	blood:	n/a	chr12:49453504-49453518
12	ELF1	chr12:49453481-49455109	GM12878	blood:	n/a	chr12:49454278-49454290
13	TCF12	chr12:49453092-49455328	ECC-1	luminal epithelium:	n/a	n/a
14	MAZ	chr12:49452677-49455391	IMR90	lung:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49453616-49453625 chr12:49454690-49454701
15	POLR2A	chr12:49452959-49455403	K562	blood:	n/a	n/a
16	TAF1	chr12:49453319-49455161	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr12:49453127-49455315	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr12:49453008-49453606	Hela-S3	cervix:	n/a	n/a
19	SIN3A	chr12:49453141-49455163	H1-hESC	embryonic stem cell:	n/a	chr12:49454951-49454960 chr12:49453619-49453629 chr12:49453369-49453382 chr12:49453620-49453633
20	TCF7L2	chr12:49453000-49454932	Hela-S3	cervix:	n/a	chr12:49453675-49453685 chr12:49453671-49453687 chr12:49453672-49453686 chr12:49453671-49453687 chr12:49453672-49453686 chr12:49453675-49453684
21	CREB1	chr12:49453382-49453816	A549	lung:	n/a	n/a
22	POLR2A	chr12:49453039-49455380	H1-hESC	embryonic stem cell:	n/a	n/a
23	YY1	chr12:49453223-49455168	HepG2	liver:	n/a	chr12:49453836-49453845 chr12:49454382-49454391 chr12:49454180-49454189 chr12:49454721-49454730
24	TAF1	chr12:49453105-49455372	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr12:49453235-49455116	NB4	blood:	n/a	n/a
26	MAZ	chr12:49453481-49455222	K562	blood:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49453616-49453625 chr12:49454690-49454701
27	MAX	chr12:49453198-49455330	Hela-S3	cervix:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49453616-49453625 chr12:49454690-49454701
28	HCFC1	chr12:49453548-49455210	K562	blood:	n/a	n/a
29	YY1	chr12:49453496-49455130	ECC-1	luminal epithelium:	n/a	chr12:49453836-49453845 chr12:49454382-49454391 chr12:49454180-49454189 chr12:49454721-49454730
30	UBTF	chr12:49453152-49454880	K562	blood:	n/a	n/a
31	POLR2A	chr12:49453525-49455216	Raji	blood:	n/a	n/a
32	POLR2A	chr12:49453548-49455253	GM12891	blood:	n/a	n/a
33	REST	chr12:49453023-49453835	A549	lung:	n/a	chr12:49453620-49453633 chr12:49453817-49453827
34	POLR2A	chr12:49453081-49455065	GM12878	blood:	n/a	n/a
35	HMGN3	chr12:49453355-49454920	K562	blood:	n/a	n/a
36	POLR2A	chr12:49453082-49455286	GM12878	blood:	n/a	n/a
37	POLR2A	chr12:49453383-49455079	HUVEC	blood vessel:	n/a	n/a
38	PML	chr12:49453154-49453900	GM12878	blood:	n/a	n/a
39	POLR2A	chr12:49452948-49453734	K562	blood:	n/a	n/a
40	HEY1	chr12:49453209-49455414	K562	blood:	n/a	chr12:49454725-49454740 chr12:49453835-49453850 chr12:49453843-49453858 chr12:49454365-49454380 chr12:49454118-49454133
41	TCF7L2	chr12:49453272-49454936	PANC-1	pancreas:	n/a	chr12:49453675-49453685 chr12:49453671-49453687 chr12:49453672-49453686 chr12:49453671-49453687 chr12:49453672-49453686 chr12:49453675-49453684
42	MAX	chr12:49453124-49455342	A549	lung:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49453616-49453625 chr12:49454690-49454701
43	POLR2A	chr12:49453494-49455396	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr12:49453334-49455138	HepG2	liver:	n/a	n/a
45	HCFC1	chr12:49452653-49455604	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr12:49453211-49455368	HepG2	liver:	n/a	n/a
47	POLR2A	chr12:49453266-49455156	GM18505	blood:	n/a	n/a
48	REST	chr12:49453219-49455259	H1-neurons	neurons:	n/a	chr12:49453620-49453633 chr12:49454132-49454145 chr12:49453817-49453827
49	POLR2A	chr12:49452842-49455301	HL-60	blood:	n/a	n/a
50	POLR2A	chr12:49453492-49455183	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49447251..49459518-chr12:49480338..49487981,17	K562	blood:
2	chr12:49446392..49469923-chr12:49518127..49527853,66	K562	blood:
3	chr12:49452282..49457106-chr12:49501761..49505806,6	K562	blood:
4	chr12:49408338..49419708-chr12:49447252..49460551,38	K562	blood:
5	chr12:49453309..49455961-chr12:49948897..49951747,2	MCF-7	breast:
6	chr12:49210248..49212975-chr12:49452451..49454269,2	MCF-7	breast:
7	chr12:49453115..49455291-chr12:49657846..49660975,4	MCF-7	breast:
8	chr12:49245786..49247623-chr12:49451692..49454310,2	MCF-7	breast:
9	chr12:49452588..49458658-chr12:49486666..49491439,6	MCF-7	breast:
10	chr12:49448896..49462070-chr12:49656751..49663992,28	K562	blood:
11	chr12:49451508..49465481-chr12:49521303..49528986,40	MCF-7	breast:
12	chr12:49453107..49454677-chr12:49580973..49582766,2	K562	blood:
13	chr12:49409714..49416851-chr12:49447402..49455499,24	MCF-7	breast:
14	chr12:49450455..49459531-chr12:49522374..49527837,16	MCF-7	breast:
15	chr12:49440399..49469923-chr12:49518291..49528303,83	K562	blood:
16	chr12:49449329..49454848-chr12:49480302..49484566,6	K562	blood:
17	chr12:49365267..49367565-chr12:49453514..49456197,2	K562	blood:
18	chr12:49453076..49457977-chr12:49485062..49491403,12	K562	blood:
19	chr12:46765603..46767339-chr12:49452531..49455344,2	K562	blood:
20	chr12:49206889..49209222-chr12:49451651..49454239,2	MCF-7	breast:
21	chr12:49450480..49457103-chr12:49487982..49492074,8	K562	blood:
22	chr12:49452655..49454232-chr8:145150875..145152586,2	MCF-7	breast:
23	chr12:49452850..49457008-chr12:49658832..49661007,5	MCF-7	breast:
24	chr12:49452631..49454255-chr12:49495979..49497484,2	MCF-7	breast:
25	chr12:49424813..49427751-chr12:49451760..49454466,2	MCF-7	breast:
26	chr12:49432703..49444457-chr12:49447982..49454860,15	MCF-7	breast:
27	chr12:49407466..49416688-chr12:49451532..49456163,12	MCF-7	breast:
28	chr12:49449335..49458365-chr12:49656751..49666981,25	K562	blood:
29	chr12:49453099..49454977-chr16:2313964..2316664,2	MCF-7	breast:

Variant related genes	Relation type
KMT2D	TF binding region
ENSG00000167535	Chromatin interaction
ENSG00000205937	Chromatin interaction
ENSG00000169884	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000139549	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000167552	Chromatin interaction
ENSG00000135519	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000179091	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	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
6	esv3360842	chr12:49452910-49455458	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	27 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	chr12:49449200-49454200	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr12:49449400-49453600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:49449400-49453800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:49449800-49453800	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr12:49450000-49453600	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr12:49450200-49455200	Active TSS	HSMMtube	muscle
7	chr12:49450600-49453600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr12:49450800-49455400	Active TSS	Fetal Kidney	kidney
9	chr12:49451200-49453600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr12:49451200-49453600	Flanking Active TSS	Liver	Liver
11	chr12:49451200-49453600	Flanking Active TSS	Colonic Mucosa	Colon
12	chr12:49451200-49454200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:49451200-49455200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr12:49451400-49455200	Active TSS	Lung	lung
15	chr12:49451600-49453600	Flanking Active TSS	Primary B cells from peripheral blood	blood
16	chr12:49451600-49453600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:49451800-49455000	Active TSS	Muscle Satellite Cultured Cells	--
18	chr12:49451800-49455000	Active TSS	GM12878-XiMat	blood
19	chr12:49451800-49455200	Active TSS	HSMM	muscle
20	chr12:49451800-49455600	Active TSS	NHDF-Ad	bronchial
21	chr12:49452000-49455000	Active TSS	Fetal Intestine Small	intestine
22	chr12:49452000-49455200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:49452000-49455200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:49452000-49455200	Active TSS	Psoas Muscle	Psoas
25	chr12:49452000-49455200	Bivalent/Poised TSS	HepG2	liver
26	chr12:49452000-49455400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr12:49452000-49455400	Active TSS	Esophagus	oesophagus
28	chr12:49452200-49455400	Active TSS	Aorta	Aorta
29	chr12:49452400-49455000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:49452400-49455200	Active TSS	Gastric	stomach
31	chr12:49452400-49455200	Active TSS	Small Intestine	intestine
32	chr12:49452400-49455200	Active TSS	A549	lung
33	chr12:49452400-49455400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:49452400-49455400	Active TSS	H9 Cell Line	embryonic stem cell
35	chr12:49452400-49455400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:49452400-49455600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:49452600-49454200	Active TSS	Right Atrium	heart
38	chr12:49452600-49455000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:49452600-49455000	Active TSS	Fetal Heart	heart
40	chr12:49452600-49455000	Active TSS	Fetal Intestine Large	intestine
41	chr12:49452600-49455000	Active TSS	Pancreas	Pancrea
42	chr12:49452600-49455000	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr12:49452600-49455200	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr12:49452600-49455400	Active TSS	Rectal Smooth Muscle	rectum
45	chr12:49452600-49455400	Active TSS	HMEC	breast
46	chr12:49452800-49453600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:49452800-49454800	Active TSS	Placenta Amnion	Placenta Amnion
48	chr12:49452800-49454800	Active TSS	Thymus	Thymus
49	chr12:49452800-49455000	Active TSS	NHEK	skin
50	chr12:49452800-49455200	Active TSS	HUES64 Cell Line	embryonic stem cell

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