Variant report

Variant	rs2237056
Chromosome Location	chr4:110623610-110623611
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	POLR2A	chr4:110623065-110625373	GM12891	blood:	n/a	n/a
2	TAF1	chr4:110623547-110624731	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr4:110622699-110625610	H1-hESC	embryonic stem cell:	n/a	n/a
4	BCLAF1	chr4:110623560-110625057	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:110623590-110624980	GM18951	blood:	n/a	n/a
6	GTF2F1	chr4:110623207-110623653	H1-hESC	embryonic stem cell:	n/a	n/a
7	RUNX3	chr4:110623584-110624933	GM12878	blood:	n/a	chr4:110623898-110623907 chr4:110623898-110623907
8	ZNF384	chr4:110623451-110623639	GM12878	blood:	n/a	n/a
9	RUNX3	chr4:110623581-110625045	GM12878	blood:	n/a	chr4:110623898-110623907 chr4:110623898-110623907
10	RELA	chr4:110623131-110625010	GM12891	blood:	n/a	chr4:110623288-110623297 chr4:110623288-110623297
11	PML	chr4:110623468-110625096	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:110623602-110625044	GM19193	blood:	n/a	n/a
13	POLR2A	chr4:110623583-110625031	GM12892	blood:	n/a	n/a
14	POLR2A	chr4:110623194-110625038	GM19099	blood:	n/a	n/a
15	POLR2A	chr4:110623578-110624206	HepG2	liver:	n/a	n/a
16	JUND	chr4:110623454-110625025	GM12878	blood:	n/a	chr4:110624053-110624065
17	TAF1	chr4:110623089-110624798	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr4:110622902-110625466	GM12878	blood:	n/a	n/a
19	ZNF384	chr4:110623377-110623641	K562	blood:	n/a	n/a
20	POLR2A	chr4:110623042-110624989	H1-hESC	embryonic stem cell:	n/a	n/a
21	EBF1	chr4:110623138-110625419	GM12878	blood:	n/a	chr4:110624832-110624843
22	RELA	chr4:110623077-110625077	GM15510	blood:	n/a	chr4:110623288-110623297 chr4:110623288-110623297
23	UBTF	chr4:110623080-110624966	K562	blood:	n/a	n/a
24	MAZ	chr4:110622909-110625527	IMR90	lung:	n/a	chr4:110623059-110623069
25	NR2F2	chr4:110623315-110624346	K562	blood:	n/a	n/a
26	POU2F2	chr4:110623519-110624345	GM12891	blood:	n/a	n/a
27	TCF12	chr4:110623594-110624933	ECC-1	luminal epithelium:	n/a	chr4:110624139-110624146 chr4:110624100-110624109
28	POLR2A	chr4:110623072-110625052	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:110622125..110626663-chr4:110647059..110653148,13	MCF-7	breast:
2	chr1:11967066..11969049-chr4:110623162..110624730,2	MCF-7	breast:
3	chr4:110621753..110625851-chr4:110723328..110725382,3	MCF-7	breast:
4	chr4:110617659..110620407-chr4:110623274..110624827,2	MCF-7	breast:
5	chr4:110614175..110617352-chr4:110621711..110624911,3	K562	blood:
6	chr4:110621463..110624410-chr4:110832783..110835223,2	K562	blood:
7	chr4:110618563..110622220-chr4:110622548..110625878,6	K562	blood:
8	chr4:110622297..110625771-chr4:110735143..110738902,5	K562	blood:
9	chr4:110621787..110624443-chr4:110734368..110736643,3	K562	blood:
10	chr4:110611889..110614128-chr4:110622707..110624451,2	MCF-7	breast:
11	chr4:110623136..110625842-chr4:110784972..110787630,2	MCF-7	breast:
12	chr4:110622109..110625008-chr4:110733953..110738254,7	MCF-7	breast:

Variant related genes	Relation type
CASP6	TF binding region
ENSG00000109534	Chromatin interaction
ENSG00000272795	Chromatin interaction
ENSG00000123739	Chromatin interaction
ENSG00000138794	Chromatin interaction
ENSG00000205403	Chromatin interaction
ENSG00000183423	Chromatin interaction
ENSG00000273447	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000138798	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10004377	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11932526	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13107296	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13127878	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1541373	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17512351	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2301717	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3087494	0.99[ASN][1000 genomes]
rs3181187	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5030534	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5030535	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5030539	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6533448	0.99[ASN][1000 genomes]
rs6533449	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6533451	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6812043	0.99[ASN][1000 genomes]
rs6831917	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7674356	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7682236	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7694620	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9992400	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv595142	chr4:110609481-110656730	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr4:110611200-110623800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr4:110622600-110624000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:110622600-110625000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr4:110622800-110623800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
5	chr4:110622800-110623800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:110622800-110623800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr4:110622800-110623800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr4:110622800-110624000	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr4:110622800-110625000	Active TSS	Brain Hippocampus Middle	brain
10	chr4:110622800-110625200	Active TSS	H9 Cell Line	embryonic stem cell
11	chr4:110622800-110625200	Active TSS	Fetal Intestine Large	intestine
12	chr4:110623000-110623800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr4:110623000-110623800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr4:110623000-110623800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr4:110623000-110623800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr4:110623000-110623800	Flanking Active TSS	Fetal Brain Female	brain
17	chr4:110623000-110624200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:110623000-110625000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:110623000-110625000	Active TSS	HepG2	liver
20	chr4:110623000-110625200	Active TSS	Fetal Kidney	kidney
21	chr4:110623000-110625200	Active TSS	NH-A	brain
22	chr4:110623200-110623800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr4:110623200-110623800	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr4:110623200-110623800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr4:110623200-110623800	Flanking Active TSS	Fetal Muscle Trunk	muscle
26	chr4:110623200-110623800	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr4:110623200-110623800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr4:110623200-110624000	Flanking Active TSS	Fetal Brain Male	brain
29	chr4:110623200-110625000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:110623200-110625000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:110623200-110625000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:110623200-110625000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:110623200-110625000	Active TSS	Placenta Amnion	Placenta Amnion
34	chr4:110623200-110625000	Active TSS	Psoas Muscle	Psoas
35	chr4:110623200-110625200	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr4:110623200-110625200	Active TSS	H1 Cell Line	embryonic stem cell
37	chr4:110623200-110625400	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr4:110623200-110625400	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr4:110623400-110623800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:110623400-110624000	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr4:110623400-110624000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:110623400-110624600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr4:110623400-110624600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:110623400-110624600	Active TSS	HMEC	breast
45	chr4:110623400-110624800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:110623400-110624800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:110623400-110624800	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr4:110623400-110624800	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr4:110623400-110624800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr4:110623400-110624800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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