Variant report

Variant	rs57940820
Chromosome Location	chr2:54342106-54342107
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:54341925-54343361	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:54342053-54343427	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr2:54341847-54343410	GM12891	blood:	n/a	n/a
4	POLR2A	chr2:54342100-54343387	Raji	blood:	n/a	n/a
5	POLR2A	chr2:54342094-54343372	GM19099	blood:	n/a	n/a
6	CUX1	chr2:54341968-54342620	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:54342096-54343439	Hela-S3	cervix:	n/a	n/a
8	MBD4	chr2:54342024-54343470	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:54341955-54343340	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr2:54341621-54343455	HepG2	liver:	n/a	n/a
11	SRF	chr2:54342075-54343520	HCT-116	colon:	n/a	n/a
12	ELK1	chr2:54342095-54343304	Hela-S3	cervix:	n/a	n/a
13	SRF	chr2:54342076-54343495	HCT-116	colon:	n/a	n/a
14	NFIC	chr2:54342006-54343296	HepG2	liver:	n/a	n/a
15	POLR2A	chr2:54342072-54343388	IMR90	lung:	n/a	n/a
16	POLR2A	chr2:54342045-54343363	GM12892	blood:	n/a	n/a
17	POLR2A	chr2:54342106-54343383	HepG2	liver:	n/a	n/a
18	POLR2A	chr2:54341963-54343356	K562	blood:	n/a	n/a
19	POLR2A	chr2:54341964-54343371	HepG2	liver:	n/a	n/a
20	CHD1	chr2:54341903-54343457	IMR90	lung:	n/a	n/a
21	POLR2A	chr2:54341803-54343446	MCF-7	breast:	n/a	n/a
22	POLR2A	chr2:54341704-54343391	HepG2	liver:	n/a	n/a
23	POLR2A	chr2:54341898-54343375	GM12878	blood:	n/a	n/a
24	HEY1	chr2:54341822-54343409	HepG2	liver:	n/a	n/a
25	NFIC	chr2:54341928-54343381	HepG2	liver:	n/a	n/a
26	POLR2A	chr2:54342091-54343599	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr2:54341937-54343651	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr2:54342078-54343377	K562	blood:	n/a	n/a
29	POLR2A	chr2:54342095-54343497	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr2:54342073-54343382	GM18505	blood:	n/a	n/a
31	POLR2A	chr2:54341975-54343391	PANC-1	pancreas:	n/a	n/a
32	MYBL2	chr2:54341649-54343366	HepG2	liver:	n/a	n/a
33	POLR2A	chr2:54341866-54343216	K562	blood:	n/a	n/a
34	HEY1	chr2:54341898-54343319	HepG2	liver:	n/a	n/a
35	POLR2A	chr2:54341881-54343405	U87	brain:	n/a	n/a
36	SRF	chr2:54341989-54343411	MCF-7	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54196743..54198781-chr2:54341566..54344110,2	K562	blood:
2	chr2:54341520..54343821-chr2:54682367..54684141,3	MCF-7	breast:
3	chr2:54341216..54345253-chr2:54347980..54351307,5	MCF-7	breast:
4	chr2:54340617..54344494-chr2:54480899..54484108,3	K562	blood:
5	chr2:54341806..54344770-chr2:54784235..54787039,2	MCF-7	breast:
6	chr2:54341515..54343973-chr2:55337394..55340042,2	MCF-7	breast:
7	chr2:54341307..54344135-chr2:54557168..54559182,2	K562	blood:
8	chr2:54342079..54343052-chr5:109024930..109025777,2	Hela-S3	cervix:
9	chr2:54341443..54343043-chr2:54557751..54559883,2	MCF-7	breast:

No data

Variant related genes	Relation type
ACYP2	TF binding region
ENSG00000177994	Chromatin interaction
ENSG00000178021	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000112893	Chromatin interaction
ENSG00000115306	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10173565	0.87[ASN][1000 genomes]
rs10186140	0.88[ASN][1000 genomes]
rs10201710	0.83[ASN][1000 genomes]
rs10206954	0.87[ASN][1000 genomes]
rs11125522	0.82[ASN][1000 genomes]
rs11689599	0.85[ASN][1000 genomes]
rs11884229	0.87[ASN][1000 genomes]
rs11884435	0.87[ASN][1000 genomes]
rs12615044	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12617094	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12620359	0.99[ASN][1000 genomes]
rs12623320	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13399590	0.82[ASN][1000 genomes]
rs13406537	0.84[ASN][1000 genomes]
rs13417064	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13425449	0.81[ASN][1000 genomes]
rs1421618	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1421619	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17045536	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2112126	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112127	0.82[ASN][1000 genomes]
rs2287640	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287644	0.97[ASN][1000 genomes]
rs2287645	0.97[ASN][1000 genomes]
rs55762565	0.83[ASN][1000 genomes]
rs55994902	0.82[ASN][1000 genomes]
rs56696975	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57437150	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57536238	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57940005	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57995357	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58125959	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59495263	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59749650	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59929874	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59936071	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60798176	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61434527	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545387	0.87[ASN][1000 genomes]
rs6713993	0.86[ASN][1000 genomes]
rs6742463	0.86[ASN][1000 genomes]
rs72800778	0.81[ASN][1000 genomes]
rs7558563	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572559	0.86[ASN][1000 genomes]
rs7574376	0.87[ASN][1000 genomes]
rs7585466	0.93[ASN][1000 genomes]
rs7593897	0.82[ASN][1000 genomes]
rs918356	0.95[ASN][1000 genomes]
rs9631060	0.86[ASN][1000 genomes]
rs977784	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1010175	chr2:54292951-54343466	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv1851003	chr2:54324701-54372931	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
11	nsv1007731	chr2:54331179-54452329	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
12	nsv535723	chr2:54331179-54452329	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
13	nsv961690	chr2:54339295-54359290	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54331200-54342400	Weak transcription	Pancreas	Pancrea
2	chr2:54331400-54342200	Weak transcription	Aorta	Aorta
3	chr2:54341200-54342200	Flanking Active TSS	Dnd41	blood
4	chr2:54341600-54342200	Enhancers	Primary T cells fromperipheralblood	blood
5	chr2:54341600-54342200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:54341600-54342200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:54341600-54342400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:54341800-54342200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:54341800-54342200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:54341800-54342200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:54341800-54342200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:54341800-54342200	Enhancers	Primary B cells from peripheral blood	blood
13	chr2:54341800-54342200	Enhancers	Primary T cells from cord blood	blood
14	chr2:54341800-54342200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr2:54341800-54342200	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr2:54341800-54342200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:54341800-54342200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:54341800-54342200	Enhancers	Adipose Nuclei	Adipose
19	chr2:54341800-54342200	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr2:54341800-54342200	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr2:54341800-54342200	Enhancers	Fetal Intestine Large	intestine
22	chr2:54341800-54342200	Flanking Active TSS	HSMMtube	muscle
23	chr2:54341800-54342200	Active TSS	NH-A	brain
24	chr2:54341800-54342400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr2:54341800-54342400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr2:54341800-54342400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:54341800-54342400	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr2:54341800-54342400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
29	chr2:54341800-54342400	Flanking Active TSS	Brain Substantia Nigra	brain
30	chr2:54341800-54342400	Flanking Active TSS	Fetal Brain Male	brain
31	chr2:54341800-54342400	Flanking Active TSS	Fetal Heart	heart
32	chr2:54341800-54342400	Flanking Active TSS	HMEC	breast
33	chr2:54341800-54342600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:54341800-54342600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:54341800-54343000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:54341800-54343200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:54341800-54343200	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr2:54341800-54343200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:54341800-54343200	Active TSS	K562	blood
40	chr2:54341800-54343400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:54341800-54343400	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr2:54341800-54343400	Active TSS	GM12878-XiMat	blood
43	chr2:54341800-54343600	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr2:54341800-54343600	Active TSS	Muscle Satellite Cultured Cells	--
45	chr2:54341800-54343600	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr2:54341800-54343600	Active TSS	A549	lung
47	chr2:54341800-54344000	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr2:54342000-54342200	Active TSS	Primary hematopoietic stem cells	blood
49	chr2:54342000-54342200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr2:54342000-54342200	Enhancers	Brain Cingulate Gyrus	brain

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