Variant report

Variant	rs12054902
Chromosome Location	chr5:118603817-118603818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:333)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:333 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:118603780-118603930	HRE	kidney:	n/a	n/a
2	RFX5	chr5:118603126-118605130	H1-hESC	embryonic stem cell:	n/a	chr5:118603838-118603847
3	CTCF	chr5:118603760-118603910	GM12871	blood:	n/a	n/a
4	YY1	chr5:118603488-118604935	H1-hESC	embryonic stem cell:	n/a	chr5:118604540-118604549 chr5:118604239-118604248 chr5:118603670-118603682
5	POLR2A	chr5:118603543-118605326	K562	blood:	n/a	n/a
6	IRF1	chr5:118603769-118605179	K562	blood:	n/a	chr5:118603945-118603959 chr5:118603881-118603894 chr5:118604437-118604451 chr5:118603942-118603954
7	YY1	chr5:118603505-118603914	H1-hESC	embryonic stem cell:	n/a	chr5:118603670-118603682
8	POLR2A	chr5:118603667-118605366	GM18951	blood:	n/a	n/a
9	CTCF	chr5:118603740-118603890	GM12873	blood:	n/a	n/a
10	CTCF	chr5:118603740-118603890	AG09309	skin:	n/a	n/a
11	CTCF	chr5:118603663-118603973	Lung_OC	lung:	n/a	n/a
12	POLR2A	chr5:118603567-118605365	GM19193	blood:	n/a	n/a
13	POU2F2	chr5:118603619-118605314	GM12878	blood:	n/a	chr5:118605293-118605306
14	YY1	chr5:118603494-118604802	GM12878	blood:	n/a	chr5:118604540-118604549 chr5:118604239-118604248 chr5:118603670-118603682
15	RFX5	chr5:118602622-118606174	SK-N-SH	brain:	n/a	chr5:118603838-118603847 chr5:118605625-118605634
16	SP1	chr5:118603605-118604819	A549	lung:	n/a	chr5:118604246-118604260
17	TEAD4	chr5:118603587-118605454	K562	blood:	n/a	n/a
18	CTCF	chr5:118603740-118603890	GM12801	blood:	n/a	n/a
19	CTCF	chr5:118603793-118603819	LNCaP	prostate:	n/a	n/a
20	CTCF	chr5:118603754-118603883	GM20000	blood:	n/a	n/a
21	SP1	chr5:118603615-118604141	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr5:118603581-118605247	IMR90	lung:	n/a	chr5:118603803-118603816 chr5:118604192-118604205
23	CTCF	chr5:118603720-118603870	SK-N-SH_RA	brain:	n/a	n/a
24	POLR2A	chr5:118603584-118604870	GM18526	blood:	n/a	n/a
25	CREB1	chr5:118603669-118604158	ECC-1	luminal epithelium:	n/a	n/a
26	TBP	chr5:118603618-118605145	HepG2	liver:	n/a	n/a
27	NR2F2	chr5:118603576-118605265	K562	blood:	n/a	n/a
28	BRCA1	chr5:118603773-118604195	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr5:118603714-118603865	SK-N-SH_RA	brain:	n/a	n/a
30	CTCF	chr5:118603720-118603870	BE2_C	brain:	n/a	n/a
31	YY1	chr5:118603552-118603899	SK-N-SH_RA	brain:	n/a	chr5:118603670-118603682
32	CTCF	chr5:118603720-118603870	AG04450	lung:	n/a	n/a
33	TBP	chr5:118603729-118605379	K562	blood:	n/a	n/a
34	CTCF	chr5:118603742-118603844	LNCaP	prostate:	n/a	n/a
35	ELF1	chr5:118603580-118604637	MCF-7	breast:	n/a	n/a
36	TBL1XR1	chr5:118603743-118604616	GM12878	blood:	n/a	n/a
37	CREB1	chr5:118603544-118604573	HepG2	liver:	n/a	n/a
38	POLR2A	chr5:118603576-118603905	GM12878	blood:	n/a	n/a
39	CTCF	chr5:118603680-118603830	NHDF-neo	bronchial:	n/a	n/a
40	CTCF	chr5:118603681-118603936	MCF-7	breast:	n/a	n/a
41	MYC	chr5:118603659-118603943	MCF10A-Er-Src	breast:	n/a	n/a
42	HCFC1	chr5:118603728-118603854	K562	blood:	n/a	n/a
43	CTCF	chr5:118603680-118603830	Hela-S3	cervix:	n/a	n/a
44	RFX5	chr5:118603231-118604555	K562	blood:	n/a	chr5:118603838-118603847
45	CTCF	chr5:118603740-118603890	HCPEpiC	choroid plexus:	n/a	n/a
46	POLR2A	chr5:118603515-118605394	K562	blood:	n/a	n/a
47	MYC	chr5:118603688-118605278	K562	blood:	n/a	n/a
48	CTCF	chr5:118603686-118603902	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr5:118603740-118603890	GM12870	blood:	n/a	n/a
50	CTCF	chr5:118603740-118603890	AG04450	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:118603804-118603854	RPTEC	kidney:	n/a
2	chr5:118603804-118603854	GM12891	blood:	n/a
3	chr5:118603804-118603854	GM12892	blood:	n/a
4	chr5:118603804-118603854	HCPEpiC	choroid plexus:	n/a
5	chr5:118603804-118603854	Hela-S3	cervix:	n/a
6	chr5:118603804-118603854	T-47D	breast:	n/a
7	chr5:118603804-118603854	HCM	heart:	n/a
8	chr5:118603804-118603854	HUVEC	blood vessel:	n/a
9	chr5:118603804-118603854	ProgFib	skin:	n/a
10	chr5:118603804-118603854	PANC-1	pancreas:	n/a
11	chr5:118603804-118603854	HPAEpiC	pulmonary alveolar:	n/a
12	chr5:118603804-118603854	HCF	heart:	n/a
13	chr5:118603804-118603854	MCF-7	breast:	n/a
14	chr5:118603804-118603854	SK-N-SH	brain:	n/a
15	chr5:118603804-118603854	SAEC	small airway:	n/a
16	chr5:118603804-118603854	Hepatocyte	liver:	n/a
17	chr5:118603804-118603854	Jurkat	blood:	n/a
18	chr5:118603804-118603854	HAEpiC	amniotic membrane:	n/a
19	chr5:118603804-118603854	HRPEpiC	eye:	n/a
20	chr5:118603804-118603854	HEEpiC	esophagus:	n/a
21	chr5:118603804-118603854	Caco-2	colon:	n/a
22	chr5:118603804-118603854	NHDF-neo	bronchial:	n/a
23	chr5:118603804-118603854	BE2_C	brain:	n/a
24	chr5:118603804-118603854	ECC-1	luminal epithelium:	n/a
25	chr5:118603804-118603854	CMK	blood:	n/a
26	chr5:118603804-118603854	SK-N-SH_RA	brain:	n/a
27	chr5:118603804-118603854	GM19239	blood:	n/a
28	chr5:118603804-118603854	LNCaP	prostate:	n/a
29	chr5:118603804-118603854	HIPEpiC	eye:	n/a
30	chr5:118603804-118603854	HCT-116	colon:	n/a
31	chr5:118603804-118603854	HMEC	breast:	n/a
32	chr5:118603804-118603854	H1-hESC	embryonic stem cell:	embryo
33	chr5:118603804-118603854	U87	brain:	n/a
34	chr5:118603804-118603854	AG04449	skin:	fetal
35	chr5:118603804-118603854	SK-N-MC	brain:	n/a
36	chr5:118603804-118603854	HL-60	blood:	n/a
37	chr5:118603804-118603854	AG09319	gingival:	n/a
38	chr5:118603804-118603854	A549	lung:	n/a
39	chr5:118603804-118603854	PFSK-1	brain:	n/a
40	chr5:118603804-118603854	HRCEpiC	kidney:	n/a
41	chr5:118603804-118603854	GM12878	blood:	n/a
42	chr5:118603804-118603854	AoSMC	blood vessel:	n/a
43	chr5:118603804-118603854	NB4	blood:	n/a
44	chr5:118603804-118603854	HRE	kidney:	n/a
45	chr5:118603804-118603854	IMR90	lung:	fetal
46	chr5:118603804-118603854	ovcar-3	ovarian:	n/a
47	chr5:118603804-118603854	HEK293	kidney:	embryo
48	chr5:118603804-118603854	PrEC	prostate:	n/a
49	chr5:118603804-118603854	BJ	skin:	n/a
50	chr5:118603804-118603854	NH-A	brain:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:118586532..118588054-chr5:118602135..118604215,2	K562	blood:
2	chr5:118323865..118326797-chr5:118601908..118603876,2	K562	blood:
3	chr5:118322938..118326606-chr5:118602920..118605792,4	MCF-7	breast:
4	chr5:118406323..118408758-chr5:118602921..118606339,4	MCF-7	breast:

No data

Variant related genes	Relation type
TNFAIP8	TF binding region
TNFAIP8	CpG island
ENSG00000172869	Chromatin interaction
ENSG00000249494	Chromatin interaction
ENSG00000169570	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1004531	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10900729	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7704111	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462426	chr5:118465249-118621672	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv599564	chr5:118465249-118621672	ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1016595	chr5:118468658-118621672	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1019788	chr5:118488501-118607405	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv537882	chr5:118488501-118607405	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2757136	chr5:118555863-118667748	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	esv2759374	chr5:118555863-118667748	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 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	chr5:118601000-118604000	Weak transcription	Fetal Heart	heart
2	chr5:118603000-118606400	Active TSS	GM12878-XiMat	blood
3	chr5:118603200-118604000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr5:118603200-118604000	Flanking Active TSS	Dnd41	blood
5	chr5:118603200-118604200	Flanking Active TSS	K562	blood
6	chr5:118603200-118604800	Active TSS	Brain Cingulate Gyrus	brain
7	chr5:118603200-118605000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:118603200-118606600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:118603400-118604000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:118603400-118604000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:118603400-118604000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr5:118603400-118604000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:118603400-118604000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:118603400-118604200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr5:118603400-118604800	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr5:118603400-118604800	Active TSS	Brain Anterior Caudate	brain
17	chr5:118603400-118604800	Active TSS	Colonic Mucosa	Colon
18	chr5:118603400-118605000	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr5:118603400-118605000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:118603400-118605000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:118603400-118605000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:118603400-118605000	Active TSS	Colon Smooth Muscle	Colon
23	chr5:118603400-118605000	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr5:118603400-118605000	Active TSS	NHDF-Ad	bronchial
25	chr5:118603400-118605200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:118603400-118605200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr5:118603400-118605200	Active TSS	Psoas Muscle	Psoas
28	chr5:118603400-118605200	Active TSS	NHLF	lung
29	chr5:118603400-118605400	Active TSS	H9 Cell Line	embryonic stem cell
30	chr5:118603400-118605400	Active TSS	HSMMtube	muscle
31	chr5:118603400-118605600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:118603400-118605600	Active TSS	Brain Angular Gyrus	brain
33	chr5:118603600-118604000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr5:118603600-118604000	Active TSS	Fetal Lung	lung
35	chr5:118603600-118604000	Flanking Active TSS	Fetal Thymus	thymus
36	chr5:118603600-118604000	Active TSS	HepG2	liver
37	chr5:118603600-118604600	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr5:118603600-118604600	Active TSS	Fetal Brain Male	brain
39	chr5:118603600-118604800	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr5:118603600-118604800	Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr5:118603600-118604800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr5:118603600-118604800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:118603600-118604800	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr5:118603600-118604800	Active TSS	Fetal Muscle Trunk	muscle
45	chr5:118603600-118605000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:118603600-118605000	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr5:118603600-118605000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr5:118603600-118605000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:118603600-118605000	Active TSS	Left Ventricle	heart
50	chr5:118603600-118605000	Active TSS	Ovary	ovary

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