Variant report

Variant	rs998587
Chromosome Location	chr2:47452710-47452711
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	RCOR1	chr2:47452470-47452947	Hela-S3	cervix:	n/a	n/a
2	FOS	chr2:47452587-47452877	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr2:47452595-47452878	MCF10A-Er-Src	breast:	n/a	chr2:47452756-47452767 chr2:47452717-47452728
4	CEBPB	chr2:47452530-47452809	K562	blood:	n/a	n/a
5	SP1	chr2:47452434-47453137	A549	lung:	n/a	chr2:47452789-47452799 chr2:47452789-47452798
6	GTF2F1	chr2:47452699-47452730	K562	blood:	n/a	n/a
7	JUN	chr2:47452501-47452937	HUVEC	blood vessel:	n/a	chr2:47452662-47452675
8	CEBPB	chr2:47452384-47452976	HepG2	liver:	n/a	n/a
9	GTF2F1	chr2:47452550-47452905	Hela-S3	cervix:	n/a	n/a
10	MAX	chr2:47452472-47453099	SK-N-SH	brain:	n/a	n/a
11	TCF12	chr2:47452336-47453145	ECC-1	luminal epithelium:	n/a	chr2:47452699-47452709 chr2:47452703-47452710
12	CEBPB	chr2:47452416-47452903	HepG2	liver:	n/a	n/a
13	ZBTB7A	chr2:47452530-47452863	HepG2	liver:	n/a	n/a
14	RAD21	chr2:47452625-47452910	IMR90	lung:	n/a	chr2:47452702-47452716
15	MAX	chr2:47452526-47452852	HepG2	liver:	n/a	n/a
16	JUND	chr2:47452409-47452910	Hela-S3	cervix:	n/a	n/a
17	ESR1	chr2:47452588-47452852	ECC-1	luminal epithelium:	n/a	chr2:47452796-47452811
18	JUND	chr2:47452497-47452947	A549	lung:	n/a	n/a
19	CEBPB	chr2:47452396-47452971	ECC-1	luminal epithelium:	n/a	n/a
20	CEBPD	chr2:47452497-47452893	HepG2	liver:	n/a	n/a
21	PBX3	chr2:47452383-47453113	SK-N-SH	brain:	n/a	n/a
22	SIN3AK20	chr2:47452558-47452829	PANC-1	pancreas:	n/a	n/a
23	KAP1	chr2:47452632-47454290	U2OS	brain:	n/a	n/a
24	PBX3	chr2:47452381-47453174	SK-N-SH	brain:	n/a	n/a
25	RFX5	chr2:47452418-47452894	HepG2	liver:	n/a	n/a
26	SP1	chr2:47452447-47453099	A549	lung:	n/a	chr2:47452789-47452799 chr2:47452789-47452798
27	FOSL2	chr2:47452479-47453100	SK-N-SH	brain:	n/a	n/a
28	EP300	chr2:47452328-47453148	ECC-1	luminal epithelium:	n/a	chr2:47452881-47452891
29	JUND	chr2:47452453-47452896	HepG2	liver:	n/a	n/a
30	FOXA2	chr2:47452374-47452935	HepG2	liver:	n/a	n/a
31	CEBPB	chr2:47452501-47452896	A549	lung:	n/a	n/a
32	POLR2A	chr2:47452411-47453047	PANC-1	pancreas:	n/a	n/a
33	EP300	chr2:47452485-47453179	SK-N-SH	brain:	n/a	chr2:47452881-47452891
34	FOXA1	chr2:47452382-47453083	HepG2	liver:	n/a	n/a
35	CHD2	chr2:47452500-47452985	Hela-S3	cervix:	n/a	n/a
36	SP1	chr2:47452391-47453083	HepG2	liver:	n/a	chr2:47452789-47452799 chr2:47452789-47452798
37	POLR2A	chr2:47452460-47452975	HUVEC	blood vessel:	n/a	n/a
38	FOXA1	chr2:47452376-47453015	HepG2	liver:	n/a	n/a
39	MAX	chr2:47452423-47453121	A549	lung:	n/a	n/a
40	EP300	chr2:47452372-47453078	HepG2	liver:	n/a	chr2:47452881-47452891
41	RCOR1	chr2:47452663-47452974	K562	blood:	n/a	n/a
42	JUN	chr2:47452496-47452952	Hela-S3	cervix:	n/a	chr2:47452662-47452675
43	MAFK	chr2:47452573-47453007	HepG2	liver:	n/a	n/a
44	TCF12	chr2:47452529-47452908	A549	lung:	n/a	chr2:47452699-47452709 chr2:47452703-47452710
45	TEAD4	chr2:47452528-47452850	HepG2	liver:	n/a	n/a
46	BHLHE40	chr2:47452675-47452967	K562	blood:	n/a	chr2:47452700-47452716
47	HDAC2	chr2:47452420-47452921	HepG2	liver:	n/a	n/a
48	RCOR1	chr2:47452389-47453835	IMR90	lung:	n/a	n/a
49	EP300	chr2:47452547-47452916	SK-N-SH_RA	brain:	n/a	chr2:47452881-47452891
50	EGR1	chr2:47452643-47452913	K562	blood:	n/a	chr2:47452784-47452797

No.	Distal block	Cell Line	Cell type
1	chr2:47399756..47406251-chr2:47447036..47455846,12	MCF-7	breast:
2	chr2:47451335..47453658-chr2:47453697..47456326,2	MCF-7	breast:
3	chr2:47399705..47406684-chr2:47448496..47456698,16	K562	blood:
4	chr2:47450042..47452844-chr2:47571562..47573553,2	MCF-7	breast:
5	chr2:47399705..47405092-chr2:47450546..47458227,19	K562	blood:

Variant related genes	Relation type
ENSG00000226087	TF binding region
ENSG00000226087	Chromatin interaction
ENSG00000234690	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000119888	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10221560	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384441	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13390912	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13430277	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72879030	0.89[ASN][1000 genomes]
rs72879063	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs815807	0.85[CEU][hapmap]

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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	esv10649	chr2:47429316-47472670	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47442600-47452800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:47445800-47452800	Weak transcription	Fetal Kidney	kidney
3	chr2:47447200-47455400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:47447600-47455000	Enhancers	NHLF	lung
5	chr2:47448000-47455400	Enhancers	Fetal Muscle Leg	muscle
6	chr2:47448800-47454200	Enhancers	Colon Smooth Muscle	Colon
7	chr2:47449400-47452800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:47449400-47453000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:47449600-47452800	Weak transcription	Brain Anterior Caudate	brain
10	chr2:47449600-47453600	Enhancers	Fetal Muscle Trunk	muscle
11	chr2:47450000-47454000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:47450000-47455600	Enhancers	Fetal Intestine Small	intestine
13	chr2:47450000-47455800	Enhancers	K562	blood
14	chr2:47450000-47456000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:47450200-47452800	Enhancers	Fetal Heart	heart
16	chr2:47450200-47453600	Enhancers	Osteobl	bone
17	chr2:47450200-47454600	Enhancers	Liver	Liver
18	chr2:47450200-47455600	Enhancers	Fetal Intestine Large	intestine
19	chr2:47450400-47453600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:47450600-47454000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:47450800-47452800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:47450800-47454200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:47451000-47453800	Enhancers	HUVEC	blood vessel
24	chr2:47451000-47455600	Enhancers	Placenta	Placenta
25	chr2:47451200-47454000	Enhancers	NHDF-Ad	bronchial
26	chr2:47451600-47452800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr2:47451600-47453400	Enhancers	Colonic Mucosa	Colon
28	chr2:47451600-47453800	Enhancers	Spleen	Spleen
29	chr2:47451600-47453800	Enhancers	NH-A	brain
30	chr2:47451600-47454000	Enhancers	Left Ventricle	heart
31	chr2:47451600-47454000	Enhancers	Psoas Muscle	Psoas
32	chr2:47451600-47454600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:47451800-47453600	Enhancers	Hela-S3	cervix
34	chr2:47451800-47453800	Enhancers	Right Atrium	heart
35	chr2:47452000-47453800	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr2:47452000-47454000	Enhancers	Adipose Nuclei	Adipose
37	chr2:47452200-47453200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr2:47452200-47453200	Enhancers	Aorta	Aorta
39	chr2:47452200-47453400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr2:47452200-47453600	Enhancers	Right Ventricle	heart
41	chr2:47452200-47453800	Enhancers	Small Intestine	intestine
42	chr2:47452200-47453800	Flanking Active TSS	HepG2	liver
43	chr2:47452200-47454000	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr2:47452200-47454000	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr2:47452200-47454200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr2:47452200-47454200	Enhancers	Ovary	ovary
47	chr2:47452200-47455400	Enhancers	Brain Hippocampus Middle	brain
48	chr2:47452200-47455800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr2:47452400-47453000	Flanking Active TSS	A549	lung
50	chr2:47452400-47453200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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