Variant report

Variant	rs2063392
Chromosome Location	chr2:54950232-54950233
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	RFX5	chr2:54950185-54950992	H1-hESC	embryonic stem cell:	n/a	chr2:54950701-54950716
2	RFX5	chr2:54949181-54951799	IMR90	lung:	n/a	chr2:54950701-54950716
3	SIX5	chr2:54950132-54950989	A549	lung:	n/a	chr2:54950598-54950607 chr2:54950600-54950609
4	GTF2F1	chr2:54949675-54950790	Hela-S3	cervix:	n/a	n/a
5	CREB1	chr2:54950161-54951117	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD2	chr2:54950121-54950958	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF263	chr2:54950020-54951506	HEK293-T-REx	kidney:	n/a	n/a
8	KAP1	chr2:54949980-54951649	HEK293	kidney:	n/a	chr2:54951554-54951562
9	CHD2	chr2:54949866-54951299	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr2:54949700-54950705	MCF10A-Er-Src	breast:	n/a	n/a
11	MXI1	chr2:54950005-54951223	Hela-S3	cervix:	n/a	n/a
12	SMARCC1	chr2:54949807-54951484	Hela-S3	cervix:	n/a	chr2:54950598-54950607
13	CCNT2	chr2:54949958-54951177	K562	blood:	n/a	n/a
14	MBD4	chr2:54950126-54950614	HepG2	liver:	n/a	n/a
15	ETS1	chr2:54950226-54950976	K562	blood:	n/a	chr2:54950596-54950609 chr2:54950547-54950560 chr2:54950597-54950610
16	EP300	chr2:54950204-54951040	HepG2	liver:	n/a	n/a
17	PML	chr2:54950088-54950677	GM12878	blood:	n/a	n/a
18	HCFC1	chr2:54950140-54951189	K562	blood:	n/a	n/a
19	POLR2A	chr2:54950101-54951155	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr2:54950184-54950689	K562	blood:	n/a	n/a
21	TAF1	chr2:54950157-54950739	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr2:54950137-54951038	SK-N-SH	brain:	n/a	n/a
23	MTA3	chr2:54949926-54951464	GM12878	blood:	n/a	n/a
24	E2F6	chr2:54949853-54951221	K562	blood:	n/a	chr2:54950402-54950413 chr2:54950557-54950572
25	FOXA1	chr2:54949911-54950370	HepG2	liver:	n/a	n/a
26	RELA	chr2:54950151-54950916	GM18951	blood:	n/a	n/a
27	TAF1	chr2:54950194-54950659	PFSK-1	brain:	n/a	n/a
28	MAX	chr2:54950144-54951461	ECC-1	luminal epithelium:	n/a	n/a
29	PAX5	chr2:54950223-54950882	GM12878	blood:	n/a	n/a
30	MXI1	chr2:54950180-54951148	GM12878	blood:	n/a	n/a
31	POLR2A	chr2:54950170-54950666	ECC-1	luminal epithelium:	n/a	n/a
32	TBP	chr2:54949826-54951040	HepG2	liver:	n/a	n/a
33	POLR2A	chr2:54950068-54951126	SK-N-MC	brain:	n/a	n/a
34	IRF1	chr2:54950003-54950741	K562	blood:	n/a	n/a
35	SP1	chr2:54950201-54951056	A549	lung:	n/a	n/a
36	TBP	chr2:54949783-54950906	K562	blood:	n/a	n/a
37	POLR2A	chr2:54950161-54950817	PANC-1	pancreas:	n/a	n/a
38	POLR2A	chr2:54949717-54952029	Raji	blood:	n/a	n/a
39	EGR1	chr2:54950232-54951061	K562	blood:	n/a	chr2:54950393-54950402 chr2:54950535-54950559 chr2:54950597-54950621
40	ETS1	chr2:54949876-54950932	A549	lung:	n/a	chr2:54950596-54950609 chr2:54950547-54950560 chr2:54950597-54950610
41	POLR2A	chr2:54950214-54950901	HUVEC	blood vessel:	n/a	n/a
42	RFX5	chr2:54949826-54951266	Hela-S3	cervix:	n/a	chr2:54950701-54950716
43	ZNF143	chr2:54949863-54950963	K562	blood:	n/a	chr2:54950598-54950607 chr2:54950535-54950554 chr2:54950600-54950609 chr2:54950540-54950558 chr2:54950605-54950620 chr2:54950598-54950616 chr2:54950401-54950411
44	TEAD4	chr2:54949831-54950711	HepG2	liver:	n/a	n/a
45	POLR2A	chr2:54950085-54951090	U87	brain:	n/a	n/a
46	POLR2A	chr2:54950015-54950850	K562	blood:	n/a	n/a
47	MAX	chr2:54950029-54951996	A549	lung:	n/a	n/a
48	RAD21	chr2:54949764-54951129	IMR90	lung:	n/a	n/a
49	POLR2A	chr2:54950187-54951053	MCF-7	breast:	n/a	n/a
50	POLR2A	chr2:54950131-54950829	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:3327939..3328820-chr2:54949942..54950545,2	Hela-S3	cervix:
2	chr10:180831..181351-chr2:54949948..54950725,2	Hela-S3	cervix:
3	chr11:68670816..68671423-chr2:54950112..54950753,2	Hela-S3	cervix:
4	chr16:24551013..24551957-chr2:54950033..54950818,2	Hela-S3	cervix:
5	chr2:54785416..54786973-chr2:54949128..54950959,2	K562	blood:

Variant related genes	Relation type
EML6	TF binding region
ENSG00000132740	Chromatin interaction
ENSG00000015171	Chromatin interaction
ENSG00000115306	Chromatin interaction
ENSG00000122257	Chromatin interaction
ENSG00000197345	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs6704882	1.00[AMR][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	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1005449	chr2:54938633-55129503	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr2:54949400-54950400	Flanking Active TSS	K562	blood
2	chr2:54949600-54950400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:54949600-54950400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:54949600-54950400	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr2:54949600-54950400	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr2:54949600-54950400	Flanking Active TSS	Dnd41	blood
7	chr2:54949600-54950400	Flanking Active TSS	Osteobl	bone
8	chr2:54949600-54950800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr2:54949600-54950800	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr2:54949600-54951200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:54949600-54951400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr2:54949800-54950400	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr2:54949800-54950400	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr2:54949800-54950400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr2:54949800-54950400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr2:54949800-54950400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr2:54949800-54950400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:54949800-54950400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr2:54949800-54950400	Flanking Active TSS	HUVEC	blood vessel
20	chr2:54949800-54950400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr2:54949800-54950800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:54949800-54951000	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr2:54949800-54951200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr2:54949800-54951200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:54949800-54951200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:54949800-54951600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:54949800-54951800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:54949800-54952600	Active TSS	Psoas Muscle	Psoas
29	chr2:54949800-54952800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr2:54950000-54950400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr2:54950000-54950400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
32	chr2:54950000-54950400	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr2:54950000-54950400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr2:54950000-54950400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr2:54950000-54950400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr2:54950000-54950400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:54950000-54950400	Flanking Active TSS	Fetal Brain Male	brain
38	chr2:54950000-54950400	Flanking Active TSS	Fetal Brain Female	brain
39	chr2:54950000-54950400	Flanking Active TSS	Fetal Lung	lung
40	chr2:54950000-54950400	Flanking Active TSS	Fetal Muscle Leg	muscle
41	chr2:54950000-54950600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr2:54950000-54950600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:54950000-54950800	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr2:54950000-54950800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:54950000-54950800	Active TSS	Fetal Muscle Trunk	muscle
46	chr2:54950000-54951000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:54950000-54951000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:54950000-54951000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:54950000-54951000	Active TSS	Fetal Intestine Small	intestine
50	chr2:54950000-54951200	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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