Variant report

Variant	rs540835012
Chromosome Location	chr3:42690900-42690901
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:42690714-42691728	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:42690900-42692078	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:42690826-42691967	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:42690844-42692305	HL-60	blood:	n/a	n/a
5	POLR2A	chr3:42690613-42691050	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr3:42690375-42691040	GM12891	blood:	n/a	n/a
7	POLR2A	chr3:42690826-42692422	K562	blood:	n/a	n/a
8	POLR2A	chr3:42690807-42691996	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:42690177-42691955	K562	blood:	n/a	n/a
10	POLR2A	chr3:42690361-42692444	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:42690757-42691954	GM12891	blood:	n/a	n/a
12	POLR2A	chr3:42687656-42693228	K562	blood:	n/a	n/a
13	POLR2A	chr3:42690273-42691883	HepG2	liver:	n/a	n/a
14	POLR2A	chr3:42690738-42691080	GM12891	blood:	n/a	n/a
15	POLR2A	chr3:42690303-42691045	GM12892	blood:	n/a	n/a
16	POLR2A	chr3:42690868-42691026	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr3:42690757-42692140	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr3:42690848-42692850	GM12891	blood:	n/a	n/a
19	POLR2A	chr3:42690795-42692430	K562	blood:	n/a	n/a
20	POLR2A	chr3:42690264-42693660	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:42690846-42692127	A549	lung:	n/a	n/a
22	POLR2A	chr3:42690191-42691572	K562	blood:	n/a	n/a
23	POLR2A	chr3:42690464-42691089	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:42655417..42657513-chr3:42690626..42693228,2	K562	blood:
2	chr3:42671852..42674989-chr3:42686737..42692314,6	K562	blood:
3	chr3:42690176..42693159-chr3:42693581..42695274,2	MCF-7	breast:
4	chr3:42688509..42691154-chr3:42691239..42693774,3	MCF-7	breast:

No data

Variant related genes	Relation type
ZBTB47	TF binding region
ENSG00000114857	Chromatin interaction
ENSG00000114853	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

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	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1818302	chr3:42688867-42709062	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv876731	chr3:42690285-42711655	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 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	chr3:42651200-42693000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:42658200-42693000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:42658400-42691400	Strong transcription	Dnd41	blood
4	chr3:42668400-42692800	Strong transcription	Fetal Muscle Trunk	muscle
5	chr3:42669200-42691800	Strong transcription	Fetal Intestine Large	intestine
6	chr3:42669200-42692200	Strong transcription	Liver	Liver
7	chr3:42669400-42691600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:42669400-42692200	Strong transcription	Fetal Muscle Leg	muscle
9	chr3:42669600-42691000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:42671200-42691400	Strong transcription	HSMM	muscle
11	chr3:42671200-42691600	Strong transcription	NH-A	brain
12	chr3:42671400-42692200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:42671400-42692200	Strong transcription	Adipose Nuclei	Adipose
14	chr3:42672000-42691800	Strong transcription	Stomach Smooth Muscle	stomach
15	chr3:42672600-42692200	Strong transcription	Fetal Brain Female	brain
16	chr3:42673200-42692600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:42674800-42692200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:42677000-42692800	Strong transcription	Fetal Stomach	stomach
19	chr3:42677600-42692600	Strong transcription	Primary hematopoietic stem cells	blood
20	chr3:42680600-42692400	Strong transcription	Fetal Intestine Small	intestine
21	chr3:42680800-42692200	Weak transcription	Right Atrium	heart
22	chr3:42681200-42691000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:42681400-42691400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:42682800-42692200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:42683200-42691000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:42683200-42692200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr3:42683800-42691000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:42683800-42691000	Strong transcription	HMEC	breast
29	chr3:42685000-42693600	Weak transcription	Stomach Mucosa	stomach
30	chr3:42686400-42692200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:42686400-42692600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:42686400-42695000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:42686600-42693800	Weak transcription	Colonic Mucosa	Colon
34	chr3:42686600-42694200	Weak transcription	Fetal Brain Male	brain
35	chr3:42686600-42694800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:42686800-42694600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:42687200-42691400	Weak transcription	Gastric	stomach
38	chr3:42687200-42692200	Weak transcription	Esophagus	oesophagus
39	chr3:42687600-42692000	Strong transcription	Primary T cells from cord blood	blood
40	chr3:42687800-42691600	Strong transcription	Colon Smooth Muscle	Colon
41	chr3:42687800-42693800	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr3:42688000-42691800	Genic enhancers	Brain Anterior Caudate	brain
43	chr3:42688000-42692000	Strong transcription	Brain Germinal Matrix	brain
44	chr3:42688000-42692600	Strong transcription	Lung	lung
45	chr3:42688200-42692600	Weak transcription	A549	lung
46	chr3:42688400-42692400	Genic enhancers	Brain Cingulate Gyrus	brain
47	chr3:42688400-42692600	Genic enhancers	Brain Inferior Temporal Lobe	brain
48	chr3:42688400-42692800	Genic enhancers	Brain Angular Gyrus	brain
49	chr3:42688600-42692000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:42688600-42694800	Weak transcription	Fetal Kidney	kidney

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