Variant report

Variant	rs2272161
Chromosome Location	chr1:77747738-77747739
allele	A/C
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	chr1:77747577-77747793	A549	lung:	n/a	n/a
2	SIN3AK20	chr1:77747582-77748455	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr1:77747620-77747770	AG04449	skin:	n/a	chr1:77747699-77747708
4	FOXP2	chr1:77747294-77748019	PFSK-1	brain:	n/a	n/a
5	CTCF	chr1:77747720-77747870	GM12873	blood:	n/a	n/a
6	CHD1	chr1:77747341-77748102	H1-hESC	embryonic stem cell:	n/a	chr1:77747549-77747559
7	ZNF143	chr1:77747380-77747968	H1-hESC	embryonic stem cell:	n/a	n/a
8	MYC	chr1:77747549-77747849	MCF10A-Er-Src	breast:	n/a	n/a
9	CTCF	chr1:77747600-77747750	HCPEpiC	choroid plexus:	n/a	chr1:77747699-77747708
10	CTCF	chr1:77747600-77747750	AG04449	skin:	n/a	chr1:77747699-77747708
11	TAF1	chr1:77747509-77748107	SK-N-SH	brain:	n/a	n/a
12	TEAD4	chr1:77747333-77747831	H1-hESC	embryonic stem cell:	n/a	n/a
13	GABPA	chr1:77747281-77747768	H1-hESC	embryonic stem cell:	n/a	n/a
14	E2F6	chr1:77747217-77748911	H1-hESC	embryonic stem cell:	n/a	chr1:77748216-77748223 chr1:77748216-77748223 chr1:77747532-77747541 chr1:77748193-77748202 chr1:77747603-77747612 chr1:77747579-77747589 chr1:77747787-77747797 chr1:77748216-77748223
15	MAX	chr1:77747300-77748303	ECC-1	luminal epithelium:	n/a	chr1:77747533-77747543
16	TAF1	chr1:77747266-77748932	H1-hESC	embryonic stem cell:	n/a	n/a
17	NFIC	chr1:77747318-77747919	ECC-1	luminal epithelium:	n/a	n/a
18	MAX	chr1:77747504-77748179	HepG2	liver:	n/a	chr1:77747533-77747543
19	REST	chr1:77746941-77748101	H1-neurons	neurons:	n/a	chr1:77747667-77747680 chr1:77746990-77747008 chr1:77747814-77747824 chr1:77747609-77747622 chr1:77747641-77747651
20	SIN3A	chr1:77747219-77749389	H1-hESC	embryonic stem cell:	n/a	chr1:77748356-77748367 chr1:77747741-77747749 chr1:77747735-77747748
21	MAX	chr1:77747255-77748854	SK-N-SH	brain:	n/a	chr1:77747533-77747543
22	YY1	chr1:77747447-77747782	SK-N-SH_RA	brain:	n/a	chr1:77747707-77747721
23	POLR2A	chr1:77747254-77748105	H1-neurons	neurons:	n/a	n/a
24	CTCF	chr1:77747640-77747790	HMEC	breast:	n/a	chr1:77747699-77747708
25	CTCF	chr1:77747700-77747850	NHDF-neo	bronchial:	n/a	n/a
26	POLR2A	chr1:77747460-77747882	Gliobla	brain:	n/a	n/a
27	POLR2A	chr1:77747572-77747813	A549	lung:	n/a	n/a
28	E2F6	chr1:77747535-77748208	A549	lung:	n/a	chr1:77748193-77748202 chr1:77747603-77747612 chr1:77747579-77747589 chr1:77747787-77747797
29	MYC	chr1:77747441-77747823	MCF-7	breast:	n/a	chr1:77747533-77747543
30	CTCF	chr1:77747679-77747742	LNCaP	prostate:	n/a	chr1:77747699-77747708
31	MAX	chr1:77747279-77748964	H1-hESC	embryonic stem cell:	n/a	chr1:77747533-77747543
32	MXI1	chr1:77747085-77749961	SK-N-SH	brain:	n/a	chr1:77748400-77748409
33	CTBP2	chr1:77747283-77749011	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr1:77747469-77748697	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:77747149-77748486	H1-neurons	neurons:	n/a	n/a
36	CTCF	chr1:77747600-77747750	HCM	heart:	n/a	chr1:77747699-77747708
37	ZBTB7A	chr1:77747275-77748169	ECC-1	luminal epithelium:	n/a	n/a
38	RAD21	chr1:77747472-77749033	IMR90	lung:	n/a	n/a
39	KAP1	chr1:77747335-77748344	HEK293	kidney:	n/a	n/a
40	YY1	chr1:77747420-77748454	SK-N-SH	brain:	n/a	chr1:77747789-77747798 chr1:77747707-77747721 chr1:77747829-77747838
41	MAX	chr1:77747294-77748277	ECC-1	luminal epithelium:	n/a	chr1:77747533-77747543
42	E2F6	chr1:77747701-77748343	A549	lung:	n/a	chr1:77748216-77748223 chr1:77748216-77748223 chr1:77748193-77748202 chr1:77747787-77747797 chr1:77748216-77748223
43	MAX	chr1:77747291-77748382	A549	lung:	n/a	chr1:77747533-77747543
44	MXI1	chr1:77747266-77748949	IMR90	lung:	n/a	chr1:77748400-77748409
45	RAD21	chr1:77747236-77748158	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAX	chr1:77747206-77749055	H1-hESC	embryonic stem cell:	n/a	chr1:77747533-77747543
47	POLR2A	chr1:77747422-77747862	HUVEC	blood vessel:	n/a	n/a
48	CTCF	chr1:77747620-77747770	HRE	kidney:	n/a	chr1:77747699-77747708
49	POLR2A	chr1:77747492-77747932	A549	lung:	n/a	n/a
50	MAZ	chr1:77747079-77749195	IMR90	lung:	n/a	chr1:77747533-77747543

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77684670..77686781-chr1:77746398..77749229,3	MCF-7	breast:

Variant related genes	Relation type
AK5	TF binding region
ENSG00000142892	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12091579	0.84[ASN][1000 genomes]
rs12095740	0.84[ASN][1000 genomes]
rs12407610	0.82[ASN][1000 genomes]
rs1592340	0.86[ASN][1000 genomes]
rs17100308	0.86[ASN][1000 genomes]
rs2815321	0.91[ASN][1000 genomes]
rs2815322	0.92[ASN][1000 genomes]
rs34422174	0.91[ASN][1000 genomes]
rs3921995	0.96[ASN][1000 genomes]
rs72641172	0.94[ASN][1000 genomes]
rs72641173	0.89[ASN][1000 genomes]
rs72641174	0.85[ASN][1000 genomes]
rs940283	0.92[ASN][1000 genomes]

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	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77745200-77747800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
2	chr1:77745600-77747800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
3	chr1:77746600-77749000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr1:77746800-77748400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:77746800-77749200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:77746800-77749400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:77746800-77749600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr1:77747000-77748000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:77747000-77748000	Bivalent/Poised TSS	HUVEC	blood vessel
10	chr1:77747000-77748200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:77747000-77748600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:77747000-77749000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
13	chr1:77747000-77749400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:77747000-77749600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr1:77747000-77750400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr1:77747000-77750600	Active TSS	Brain Substantia Nigra	brain
17	chr1:77747200-77747800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:77747200-77747800	Bivalent/Poised TSS	Fetal Brain Female	brain
19	chr1:77747200-77747800	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
20	chr1:77747200-77747800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
21	chr1:77747200-77748000	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr1:77747200-77748000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:77747200-77748000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
24	chr1:77747200-77748000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
25	chr1:77747200-77748000	Bivalent/Poised TSS	NHEK	skin
26	chr1:77747200-77748200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr1:77747200-77748200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
28	chr1:77747200-77748200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
29	chr1:77747200-77748200	Active TSS	NH-A	brain
30	chr1:77747200-77748400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:77747200-77748600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:77747200-77748600	Active TSS	Brain Anterior Caudate	brain
33	chr1:77747200-77748800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:77747200-77748800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:77747200-77748800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
36	chr1:77747200-77748800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
37	chr1:77747200-77748800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
38	chr1:77747200-77748800	Active TSS	A549	lung
39	chr1:77747200-77749000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:77747200-77749000	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr1:77747200-77749000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:77747200-77749000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
43	chr1:77747200-77749000	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr1:77747200-77749000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
45	chr1:77747200-77749000	Active TSS	NHLF	lung
46	chr1:77747200-77749200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr1:77747200-77749200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:77747200-77749200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:77747200-77749200	Active TSS	HSMM	muscle
50	chr1:77747200-77749200	Active TSS	HSMMtube	muscle

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