Variant report

Variant	rs34272251
Chromosome Location	chr2:54951036-54951037
allele	CT/TC
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	chr2:54949181-54951799	IMR90	lung:	n/a	chr2:54950701-54950716
2	CTCF	chr2:54950900-54951050	GM12873	blood:	n/a	n/a
3	SIN3AK20	chr2:54950294-54951146	PANC-1	pancreas:	n/a	n/a
4	CREB1	chr2:54950161-54951117	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr2:54950250-54951059	GM15510	blood:	n/a	n/a
6	ZNF263	chr2:54950020-54951506	HEK293-T-REx	kidney:	n/a	n/a
7	POLR2A	chr2:54950671-54951050	A549	lung:	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	MXI1	chr2:54950005-54951223	Hela-S3	cervix:	n/a	n/a
11	SMARCC1	chr2:54949807-54951484	Hela-S3	cervix:	n/a	chr2:54950598-54950607
12	CCNT2	chr2:54949958-54951177	K562	blood:	n/a	n/a
13	RAD21	chr2:54950891-54951091	HepG2	liver:	n/a	n/a
14	EP300	chr2:54950204-54951040	HepG2	liver:	n/a	n/a
15	HMGN3	chr2:54950306-54951340	K562	blood:	n/a	n/a
16	TCF12	chr2:54950261-54951067	ECC-1	luminal epithelium:	n/a	n/a
17	HCFC1	chr2:54950140-54951189	K562	blood:	n/a	n/a
18	ZKSCAN1	chr2:54950473-54951092	Hela-S3	cervix:	n/a	n/a
19	TCF7L2	chr2:54950308-54951202	HCT-116	colon:	n/a	n/a
20	POLR2A	chr2:54950101-54951155	Hela-S3	cervix:	n/a	n/a
21	MAX	chr2:54950137-54951038	SK-N-SH	brain:	n/a	n/a
22	MTA3	chr2:54949926-54951464	GM12878	blood:	n/a	n/a
23	E2F6	chr2:54949853-54951221	K562	blood:	n/a	chr2:54950402-54950413 chr2:54950557-54950572
24	HDAC2	chr2:54950266-54951203	MCF-7	breast:	n/a	n/a
25	CTCF	chr2:54950896-54951070	H1-hESC	embryonic stem cell:	n/a	n/a
26	E2F6	chr2:54950619-54951112	K562	blood:	n/a	n/a
27	BACH1	chr2:54950247-54951369	H1-hESC	embryonic stem cell:	n/a	n/a
28	EBF1	chr2:54950709-54951152	GM12878	blood:	n/a	n/a
29	MAX	chr2:54950144-54951461	ECC-1	luminal epithelium:	n/a	n/a
30	CTCF	chr2:54950900-54951050	HUVEC	blood vessel:	n/a	n/a
31	MXI1	chr2:54950180-54951148	GM12878	blood:	n/a	n/a
32	CTCF	chr2:54950876-54951055	Spleen_OC	spleen:	n/a	n/a
33	CTCF	chr2:54950876-54951043	SK-N-SH_RA	brain:	n/a	n/a
34	TBP	chr2:54949826-54951040	HepG2	liver:	n/a	n/a
35	POLR2A	chr2:54950068-54951126	SK-N-MC	brain:	n/a	n/a
36	CTCF	chr2:54950940-54951090	NB4	blood:	n/a	n/a
37	SP1	chr2:54950201-54951056	A549	lung:	n/a	n/a
38	POLR2A	chr2:54949717-54952029	Raji	blood:	n/a	n/a
39	POLR2A	chr2:54950241-54951129	HEK293	kidney:	n/a	n/a
40	CTCF	chr2:54950900-54951050	AG04450	lung:	n/a	n/a
41	CTCF	chr2:54950960-54951110	HMEC	breast:	n/a	n/a
42	CTCF	chr2:54950920-54951070	AG04449	skin:	n/a	n/a
43	CTCF	chr2:54950880-54951079	MCF-7	breast:	n/a	n/a
44	CTCF	chr2:54950900-54951050	GM12878	blood:	n/a	n/a
45	CTCF	chr2:54950909-54951068	Hela-S3	cervix:	n/a	n/a
46	EGR1	chr2:54950232-54951061	K562	blood:	n/a	chr2:54950393-54950402 chr2:54950535-54950559 chr2:54950597-54950621
47	CTCF	chr2:54950980-54951130	BJ	skin:	n/a	n/a
48	TCF3	chr2:54950488-54951192	GM12878	blood:	n/a	n/a
49	CTCF	chr2:54950920-54951070	NHDF-neo	bronchial:	n/a	n/a
50	RFX5	chr2:54949826-54951266	Hela-S3	cervix:	n/a	chr2:54950701-54950716

Variant related genes	Relation type
EML6	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10169439	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10194108	0.80[EUR][1000 genomes]
rs11883962	0.82[EUR][1000 genomes]
rs11888644	0.84[ASN][1000 genomes]
rs13419761	0.89[ASN][1000 genomes]
rs13428703	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17046257	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58878579	0.88[ASN][1000 genomes]
rs6545440	0.84[ASN][1000 genomes]
rs6708082	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6732751	0.83[ASN][1000 genomes]
rs6740110	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6752720	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6753004	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67909358	0.82[EUR][1000 genomes]
rs7582640	0.82[EUR][1000 genomes];0.85[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	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	chr2:54949600-54951200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:54949600-54951400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr2:54949800-54951200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr2:54949800-54951200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:54949800-54951200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:54949800-54951600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:54949800-54951800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:54949800-54952600	Active TSS	Psoas Muscle	Psoas
9	chr2:54949800-54952800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr2:54950000-54951200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr2:54950000-54951200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr2:54950000-54951200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:54950000-54951200	Active TSS	Placenta	Placenta
14	chr2:54950000-54951200	Active TSS	A549	lung
15	chr2:54950000-54952000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:54950000-54952000	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr2:54950000-54952200	Active TSS	Esophagus	oesophagus
18	chr2:54950000-54952200	Active TSS	Gastric	stomach
19	chr2:54950000-54952200	Active TSS	Left Ventricle	heart
20	chr2:54950000-54952200	Active TSS	Lung	lung
21	chr2:54950000-54952400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:54950000-54952400	Active TSS	Aorta	Aorta
23	chr2:54950000-54952600	Active TSS	Right Atrium	heart
24	chr2:54950000-54952600	Active TSS	Right Ventricle	heart
25	chr2:54950000-54953400	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr2:54950200-54951200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:54950200-54951200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:54950200-54951200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:54950200-54951200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:54950200-54951200	Active TSS	Muscle Satellite Cultured Cells	--
31	chr2:54950200-54951200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
32	chr2:54950200-54951200	Active TSS	Colon Smooth Muscle	Colon
33	chr2:54950200-54951200	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr2:54950200-54951200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr2:54950200-54951200	Active TSS	Fetal Kidney	kidney
36	chr2:54950200-54951200	Bivalent/Poised TSS	Fetal Stomach	stomach
37	chr2:54950200-54951200	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr2:54950200-54951200	Active TSS	Thymus	Thymus
39	chr2:54950200-54951200	Active TSS	Hela-S3	cervix
40	chr2:54950200-54951200	Bivalent/Poised TSS	HepG2	liver
41	chr2:54950200-54951200	Active TSS	HSMM	muscle
42	chr2:54950200-54951200	Active TSS	HSMMtube	muscle
43	chr2:54950200-54951200	Active TSS	NHEK	skin
44	chr2:54950200-54951400	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr2:54950200-54951400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:54950200-54951400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:54950200-54951600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:54950200-54952000	Active TSS	Small Intestine	intestine
49	chr2:54950200-54952200	Active TSS	Pancreas	Pancrea
50	chr2:54950200-54952200	Active TSS	Spleen	Spleen

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