Variant report

Variant	rs2227746
Chromosome Location	chr5:76012355-76012356
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	TAF1	chr5:76011769-76012570	H1-hESC	embryonic stem cell:	n/a	n/a
2	TBP	chr5:76011714-76012395	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:76011809-76012996	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr5:76011671-76013008	H1-hESC	embryonic stem cell:	n/a	n/a
5	HCFC1	chr5:76011698-76012834	K562	blood:	n/a	n/a
6	TAF1	chr5:76011391-76013083	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr5:76012346-76012573	K562	blood:	n/a	n/a
8	MAX	chr5:76011027-76012490	A549	lung:	n/a	n/a
9	POLR2A	chr5:76011041-76015191	HUVEC	blood vessel:	n/a	n/a
10	MXI1	chr5:76011261-76012548	HepG2	liver:	n/a	n/a
11	TBL1XR1	chr5:76011653-76012360	GM12878	blood:	n/a	n/a
12	MYC	chr5:76011742-76013297	K562	blood:	n/a	n/a
13	CREB1	chr5:76011651-76012434	HepG2	liver:	n/a	n/a
14	POLR2A	chr5:76010271-76012979	SK-N-MC	brain:	n/a	n/a
15	SIN3AK20	chr5:76011382-76012952	SK-N-SH	brain:	n/a	n/a
16	YY1	chr5:76011677-76012552	K562	blood:	n/a	chr5:76011742-76011756
17	CCNT2	chr5:76011492-76012388	K562	blood:	n/a	n/a
18	CTBP2	chr5:76010586-76012942	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr5:76011743-76012525	H1-hESC	embryonic stem cell:	n/a	n/a
20	MXI1	chr5:76011837-76012956	GM12878	blood:	n/a	n/a
21	POLR2A	chr5:76011755-76012386	A549	lung:	n/a	n/a
22	MAX	chr5:76011110-76012428	GM12878	blood:	n/a	n/a
23	HMGN3	chr5:76011096-76012362	K562	blood:	n/a	n/a
24	SIN3A	chr5:76011220-76012878	H1-hESC	embryonic stem cell:	n/a	n/a
25	TAF1	chr5:76012345-76012646	K562	blood:	n/a	n/a
26	ELF1	chr5:76011726-76012570	GM12878	blood:	n/a	chr5:76011742-76011754
27	MAX	chr5:76010941-76012440	HepG2	liver:	n/a	n/a
28	SP1	chr5:76011641-76012440	A549	lung:	n/a	chr5:76011837-76011849 chr5:76011838-76011847 chr5:76012087-76012096 chr5:76011837-76011849
29	UBTF	chr5:76011513-76012966	K562	blood:	n/a	n/a
30	MAX	chr5:76010977-76012620	SK-N-SH	brain:	n/a	n/a
31	RAD21	chr5:76011406-76013012	IMR90	lung:	n/a	chr5:76011740-76011753
32	RAD21	chr5:76011501-76012463	H1-hESC	embryonic stem cell:	n/a	chr5:76011740-76011753
33	RAD21	chr5:76011586-76012516	HCT-116	colon:	n/a	chr5:76011740-76011753
34	POLR2A	chr5:76010938-76016234	HUVEC	blood vessel:	n/a	n/a
35	MYC	chr5:76011982-76012861	H1-hESC	embryonic stem cell:	n/a	n/a
36	MYC	chr5:76011499-76013329	K562	blood:	n/a	n/a
37	POLR2A	chr5:76011505-76012429	K562	blood:	n/a	n/a
38	POLR2A	chr5:76011173-76015204	SK-N-SH	brain:	n/a	n/a
39	POU2F2	chr5:76011775-76012437	GM12878	blood:	n/a	n/a
40	ELF1	chr5:76012311-76012538	K562	blood:	n/a	n/a
41	STAT1	chr5:76012217-76012476	GM12878	blood:	n/a	n/a
42	CTCF	chr5:76011664-76012516	K562	blood:	n/a	n/a
43	TCF12	chr5:76011143-76012714	A549	lung:	n/a	chr5:76011540-76011550
44	CTCF	chr5:76011162-76012407	A549	lung:	n/a	chr5:76011189-76011202
45	WRNIP1	chr5:76012238-76012397	GM12878	blood:	n/a	n/a
46	MAZ	chr5:76010911-76012665	IMR90	lung:	n/a	n/a
47	MAX	chr5:76011412-76012954	K562	blood:	n/a	n/a
48	REST	chr5:76011543-76013114	H1-neurons	neurons:	n/a	chr5:76012745-76012755 chr5:76012077-76012090 chr5:76011543-76011556 chr5:76011964-76011971 chr5:76012111-76012124
49	CTCF	chr5:76010894-76012734	SK-N-SH	brain:	n/a	chr5:76011189-76011202
50	CTCF	chr5:76012340-76012490	AG04450	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75997956..76000044-chr5:76012205..76013755,2	K562	blood:

Variant related genes	Relation type
ENSG00000225407	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17681908	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2227749	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227753	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2227757	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61370375	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61557265	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73127565	0.91[AMR][1000 genomes]
rs73127576	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs73127579	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73127582	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73127587	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73127593	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73127597	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1035135	chr5:75927027-76092058	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv882207	chr5:75997213-76027823	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv882208	chr5:75997213-76034355	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv882209	chr5:76004933-76034355	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr5:76010400-76012400	Flanking Bivalent TSS/Enh	Dnd41	blood
2	chr5:76010400-76013000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:76010400-76015000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:76010600-76012600	Bivalent/Poised TSS	HepG2	liver
5	chr5:76010600-76012800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr5:76010600-76013000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr5:76010600-76013200	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr5:76010600-76014200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:76010800-76012800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr5:76010800-76012800	Flanking Active TSS	Liver	Liver
11	chr5:76010800-76013000	Active TSS	Brain Substantia Nigra	brain
12	chr5:76010800-76013200	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr5:76010800-76013600	Active TSS	NHDF-Ad	bronchial
14	chr5:76011000-76012400	Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr5:76011000-76012400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:76011000-76012400	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
17	chr5:76011000-76012800	Bivalent/Poised TSS	Esophagus	oesophagus
18	chr5:76011000-76013000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
19	chr5:76011000-76013000	Active TSS	Ovary	ovary
20	chr5:76011000-76013400	Active TSS	A549	lung
21	chr5:76011000-76013600	Active TSS	NHLF	lung
22	chr5:76011200-76012400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
23	chr5:76011200-76012600	Bivalent/Poised TSS	Fetal Stomach	stomach
24	chr5:76011200-76013000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:76011200-76013000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:76011200-76013000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:76011200-76013000	Active TSS	Aorta	Aorta
28	chr5:76011200-76013200	Active TSS	H9 Cell Line	embryonic stem cell
29	chr5:76011200-76013400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:76011200-76013400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:76011200-76013400	Active TSS	K562	blood
32	chr5:76011200-76013600	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr5:76011200-76014400	Active TSS	Fetal Kidney	kidney
34	chr5:76011400-76012400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr5:76011400-76012600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
36	chr5:76011400-76012600	Active TSS	Duodenum Mucosa	Duodenum
37	chr5:76011400-76012600	Active TSS	Hela-S3	cervix
38	chr5:76011400-76012800	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr5:76011400-76013000	Active TSS	Small Intestine	intestine
40	chr5:76011400-76013200	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr5:76011400-76013600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:76011600-76012400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr5:76011600-76012400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:76011600-76012400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:76011600-76012600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:76011600-76012600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:76011600-76012600	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr5:76011600-76012600	Active TSS	Muscle Satellite Cultured Cells	--
49	chr5:76011600-76012600	Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr5:76011600-76012600	Active TSS	Pancreas	Pancrea

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