Variant report

Variant	rs562527677
Chromosome Location	chr3:51741211-51741212
allele	A/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	REST	chr3:51740438-51741739	H1-neurons	neurons:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
2	TAF1	chr3:51740824-51741410	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr3:51740473-51741350	HL-60	blood:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
4	E2F6	chr3:51740850-51741682	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:51740823-51741460	SK-N-MC	brain:	n/a	n/a
6	REST	chr3:51740410-51741624	PFSK-1	brain:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
7	MXI1	chr3:51740630-51741603	IMR90	lung:	n/a	n/a
8	REST	chr3:51741051-51741222	K562	blood:	n/a	chr3:51741059-51741072
9	TBP	chr3:51740818-51741572	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:51740868-51741318	MCF-7	breast:	n/a	n/a
11	POLR2A	chr3:51740877-51741224	HUVEC	blood vessel:	n/a	n/a
12	MXI1	chr3:51740770-51741480	H1-hESC	embryonic stem cell:	n/a	n/a
13	ZBTB7A	chr3:51741003-51741439	ECC-1	luminal epithelium:	n/a	n/a
14	REST	chr3:51740538-51741286	HepG2	liver:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
15	REST	chr3:51740204-51741740	PFSK-1	brain:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740250-51740259 chr3:51740897-51740906
16	REST	chr3:51739816-51741537	SK-N-SH	brain:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740250-51740259 chr3:51740897-51740906
17	REST	chr3:51740712-51741250	HepG2	liver:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
18	TAF7	chr3:51740777-51741292	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr3:51740745-51741379	H1-neurons	neurons:	n/a	n/a
20	MAX	chr3:51740682-51741445	ECC-1	luminal epithelium:	n/a	chr3:51740769-51740778
21	POLR2A	chr3:51741056-51741260	ECC-1	luminal epithelium:	n/a	n/a
22	MAX	chr3:51740643-51741480	ECC-1	luminal epithelium:	n/a	chr3:51740769-51740778
23	REST	chr3:51741034-51741252	GM12878	blood:	n/a	chr3:51741059-51741072
24	POLR2A	chr3:51740885-51741462	MCF-7	breast:	n/a	n/a
25	MAX	chr3:51740794-51741623	H1-hESC	embryonic stem cell:	n/a	n/a
26	ZNF263	chr3:51740825-51741351	HEK293-T-REx	kidney:	n/a	n/a
27	REST	chr3:51741083-51741284	SK-N-SH	brain:	n/a	n/a
28	TAF1	chr3:51741024-51741287	H1-hESC	embryonic stem cell:	n/a	n/a
29	REST	chr3:51740477-51741284	PANC-1	pancreas:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
30	REST	chr3:51740063-51741723	PFSK-1	brain:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740250-51740259 chr3:51740897-51740906
31	POLR2A	chr3:51741034-51741407	MCF-7	breast:	n/a	n/a
32	POLR2A	chr3:51740788-51741608	H1-neurons	neurons:	n/a	n/a
33	REST	chr3:51740699-51741211	H1-neurons	neurons:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
34	POLR2A	chr3:51741185-51741235	HepG2	liver:	n/a	n/a
35	REST	chr3:51740070-51741651	H1-hESC	embryonic stem cell:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740250-51740259 chr3:51740897-51740906
36	E2F6	chr3:51740935-51741594	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr3:51741021-51741305	ECC-1	luminal epithelium:	n/a	n/a
38	GABPA	chr3:51741042-51741448	H1-hESC	embryonic stem cell:	n/a	chr3:51741075-51741084
39	POLR2A	chr3:51741074-51741314	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAZ	chr3:51740612-51741318	IMR90	lung:	n/a	chr3:51740769-51740778
41	REST	chr3:51740414-51741265	PANC-1	pancreas:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
42	MXI1	chr3:51739763-51741816	SK-N-SH	brain:	n/a	n/a
43	REST	chr3:51740479-51741583	MCF-7	breast:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
44	POLR2A	chr3:51741033-51741263	H1-hESC	embryonic stem cell:	n/a	n/a
45	TCF12	chr3:51740784-51741430	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr3:51740862-51741458	H1-hESC	embryonic stem cell:	n/a	n/a
47	TAF1	chr3:51741018-51741339	H1-neurons	neurons:	n/a	n/a
48	MAX	chr3:51740747-51741521	H1-hESC	embryonic stem cell:	n/a	chr3:51740769-51740778
49	MYC	chr3:51740776-51741469	H1-hESC	embryonic stem cell:	n/a	n/a
50	HA-E2F1	chr3:51741112-51741530	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51739711..51741988-chr3:51976226..51978640,2	K562	blood:

Variant related genes	Relation type
GRM2	TF binding region
ENSG00000041880	Chromatin interaction

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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv1814919	chr3:51703488-51752684	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv3410055	chr3:51737012-51741510	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3403870	chr3:51740262-51741860	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51733000-51741400	Weak transcription	Fetal Heart	heart
2	chr3:51734600-51741400	Weak transcription	Fetal Lung	lung
3	chr3:51734600-51741600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:51736400-51741400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:51738400-51743400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:51738800-51741400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:51739400-51741400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:51739400-51743400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:51739600-51743600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:51739800-51741400	Weak transcription	Primary B cells from cord blood	blood
11	chr3:51739800-51741400	Weak transcription	Liver	Liver
12	chr3:51740000-51741400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:51740000-51741600	Weak transcription	Aorta	Aorta
14	chr3:51740000-51744200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr3:51740200-51746200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:51740200-51755400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:51740400-51742000	Enhancers	Spleen	Spleen
18	chr3:51740400-51742800	Weak transcription	Dnd41	blood
19	chr3:51740600-51741600	Active TSS	Fetal Brain Female	brain
20	chr3:51740600-51741600	Enhancers	Lung	lung
21	chr3:51740600-51752800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:51740800-51741400	Active TSS	HSMM	muscle
23	chr3:51740800-51746600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:51741000-51741400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:51741000-51741400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:51741000-51741400	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr3:51741000-51741400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:51741000-51741400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:51741000-51741400	Flanking Active TSS	Colonic Mucosa	Colon
30	chr3:51741000-51741400	Active TSS	Ovary	ovary
31	chr3:51741000-51741400	Flanking Active TSS	Right Atrium	heart
32	chr3:51741000-51741400	Flanking Active TSS	Right Ventricle	heart
33	chr3:51741000-51741600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
34	chr3:51741000-51741600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:51741000-51741600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
36	chr3:51741000-51741600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr3:51741000-51741600	Active TSS	Stomach Smooth Muscle	stomach
38	chr3:51741000-51741800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
39	chr3:51741000-51741800	Enhancers	Brain Anterior Caudate	brain
40	chr3:51741000-51742000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
41	chr3:51741000-51742200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
42	chr3:51741200-51741400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:51741200-51741400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:51741200-51741400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:51741200-51741400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:51741200-51741400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:51741200-51741400	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:51741200-51741400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:51741200-51741400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:51741200-51741400	Active TSS	Primary T cells from cord blood	blood

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