Variant report

Variant	rs538478346
Chromosome Location	chr1:211589988-211589989
allele	C/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	TAF1	chr1:211589551-211590383	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:211589710-211590402	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:211589535-211590698	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:211589592-211590002	GM12878	blood:	n/a	n/a
5	TAF1	chr1:211589561-211590333	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:211589693-211590651	HepG2	liver:	n/a	n/a
7	TBP	chr1:211589619-211590367	H1-hESC	embryonic stem cell:	n/a	n/a
8	YY1	chr1:211589607-211590409	HepG2	liver:	n/a	chr1:211590286-211590295
9	POLR2A	chr1:211589431-211590586	ProgFib	skin:	n/a	n/a
10	HA-E2F1	chr1:211589507-211590489	MCF-7	breast:	n/a	chr1:211590286-211590295 chr1:211589820-211589829
11	MAZ	chr1:211589501-211590470	IMR90	lung:	n/a	chr1:211589803-211589813 chr1:211590325-211590334
12	JUND	chr1:211589575-211590040	A549	lung:	n/a	n/a
13	POLR2A	chr1:211589575-211590284	MCF-7	breast:	n/a	n/a
14	POLR2A	chr1:211589461-211590384	MCF-7	breast:	n/a	n/a
15	POLR2A	chr1:211589511-211590066	PANC-1	pancreas:	n/a	n/a
16	MAX	chr1:211589813-211590492	HepG2	liver:	n/a	chr1:211590325-211590334 chr1:211590461-211590471
17	POLR2A	chr1:211589601-211590007	A549	lung:	n/a	n/a
18	POLR2A	chr1:211589419-211590420	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr1:211589503-211590370	MCF-7	breast:	n/a	n/a
20	POLR2A	chr1:211589558-211590522	A549	lung:	n/a	n/a
21	FOXA2	chr1:211589542-211590010	A549	lung:	n/a	n/a
22	POLR2A	chr1:211589419-211590263	GM12878	blood:	n/a	n/a
23	HEY1	chr1:211589599-211590041	HepG2	liver:	n/a	chr1:211589815-211589830 chr1:211589745-211589760 chr1:211589825-211589840
24	TAF1	chr1:211589553-211590422	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr1:211589944-211590318	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr1:211589462-211589989	K562	blood:	n/a	n/a
27	POLR2A	chr1:211589421-211590049	HUVEC	blood vessel:	n/a	n/a
28	RAD21	chr1:211589469-211590450	H1-hESC	embryonic stem cell:	n/a	chr1:211590289-211590301 chr1:211589686-211589700
29	TAF1	chr1:211589586-211590254	HepG2	liver:	n/a	n/a
30	MXI1	chr1:211589961-211590809	IMR90	lung:	n/a	n/a
31	POLR2A	chr1:211589549-211590312	A549	lung:	n/a	n/a
32	POLR2A	chr1:211589544-211590070	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr1:211589572-211590346	A549	lung:	n/a	n/a
34	POLR2A	chr1:211589543-211590298	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:211589512-211590692	HepG2	liver:	n/a	n/a
36	POLR2A	chr1:211589374-211590610	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
SNX25P1	TF binding region

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762141	chr1:211538685-211603843	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	esv1824154	chr1:211565640-211614280	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
3	esv3362349	chr1:211588754-211591702	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	esv3433824	chr1:211589079-211591127	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211581400-211608200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:211581800-211590600	Weak transcription	Fetal Intestine Small	intestine
3	chr1:211585400-211593200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:211589200-211590200	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr1:211589200-211590400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:211589200-211590400	Enhancers	Primary B cells from cord blood	blood
7	chr1:211589200-211590400	Active TSS	Muscle Satellite Cultured Cells	--
8	chr1:211589200-211590400	Active TSS	Adipose Nuclei	Adipose
9	chr1:211589200-211590400	Active TSS	Duodenum Mucosa	Duodenum
10	chr1:211589200-211590400	Active TSS	NH-A	brain
11	chr1:211589200-211590600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:211589200-211590800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:211589400-211590000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr1:211589400-211590200	Active TSS	Brain Angular Gyrus	brain
15	chr1:211589400-211590200	Active TSS	Brain Cingulate Gyrus	brain
16	chr1:211589400-211590200	Active TSS	Fetal Intestine Large	intestine
17	chr1:211589400-211590200	Active TSS	Stomach Smooth Muscle	stomach
18	chr1:211589400-211590200	Active TSS	HMEC	breast
19	chr1:211589400-211590400	Active TSS	H1 Cell Line	embryonic stem cell
20	chr1:211589400-211590400	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr1:211589400-211590400	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr1:211589400-211590400	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr1:211589400-211590400	Active TSS	Primary T cells from cord blood	blood
24	chr1:211589400-211590400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:211589400-211590400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:211589400-211590400	Active TSS	Brain Anterior Caudate	brain
27	chr1:211589400-211590400	Active TSS	Brain Germinal Matrix	brain
28	chr1:211589400-211590400	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr1:211589400-211590400	Active TSS	Psoas Muscle	Psoas
30	chr1:211589400-211590400	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr1:211589400-211590400	Active TSS	HepG2	liver
32	chr1:211589400-211590400	Active TSS	HSMM	muscle
33	chr1:211589400-211590400	Active TSS	HUVEC	blood vessel
34	chr1:211589400-211590400	Active TSS	NHEK	skin
35	chr1:211589400-211590400	Active TSS	Osteobl	bone
36	chr1:211589400-211590600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:211589400-211590600	Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr1:211589400-211590600	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr1:211589400-211590600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:211589400-211590600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr1:211589400-211590600	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr1:211589400-211590600	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr1:211589400-211590600	Active TSS	A549	lung
44	chr1:211589400-211590600	Active TSS	NHDF-Ad	bronchial
45	chr1:211589400-211591000	Active TSS	Brain Hippocampus Middle	brain
46	chr1:211589600-211590000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:211589600-211590000	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr1:211589600-211590200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:211589600-211590200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:211589600-211590200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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