Variant report

Variant	rs1553542
Chromosome Location	chr5:118604237-118604238
allele	A/C
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	chr5:118603126-118605130	H1-hESC	embryonic stem cell:	n/a	chr5:118603838-118603847
2	YY1	chr5:118603488-118604935	H1-hESC	embryonic stem cell:	n/a	chr5:118604540-118604549 chr5:118604239-118604248 chr5:118603670-118603682
3	POLR2A	chr5:118603543-118605326	K562	blood:	n/a	n/a
4	RAD21	chr5:118604137-118604487	K562	blood:	n/a	chr5:118604192-118604205
5	YY1	chr5:118604088-118604788	K562	blood:	n/a	chr5:118604540-118604549 chr5:118604239-118604248
6	IRF1	chr5:118603769-118605179	K562	blood:	n/a	chr5:118603945-118603959 chr5:118603881-118603894 chr5:118604437-118604451 chr5:118603942-118603954
7	SIN3AK20	chr5:118604105-118604840	PANC-1	pancreas:	n/a	n/a
8	YY1	chr5:118603875-118604471	A549	lung:	n/a	chr5:118604239-118604248
9	POLR2A	chr5:118603667-118605366	GM18951	blood:	n/a	n/a
10	REST	chr5:118603935-118604881	A549	lung:	n/a	chr5:118604555-118604573
11	POLR2A	chr5:118603840-118605364	Raji	blood:	n/a	n/a
12	CREB1	chr5:118604076-118604805	A549	lung:	n/a	n/a
13	MXI1	chr5:118604227-118605384	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr5:118603567-118605365	GM19193	blood:	n/a	n/a
15	UBTF	chr5:118604095-118605240	K562	blood:	n/a	n/a
16	POU2F2	chr5:118603619-118605314	GM12878	blood:	n/a	chr5:118605293-118605306
17	STAT5A	chr5:118603874-118605378	GM12878	blood:	n/a	chr5:118604247-118604259 chr5:118605109-118605116
18	YY1	chr5:118603494-118604802	GM12878	blood:	n/a	chr5:118604540-118604549 chr5:118604239-118604248 chr5:118603670-118603682
19	MYC	chr5:118604165-118604647	MCF-7	breast:	n/a	n/a
20	RFX5	chr5:118602622-118606174	SK-N-SH	brain:	n/a	chr5:118603838-118603847 chr5:118605625-118605634
21	POLR2A	chr5:118604031-118604651	SK-N-SH	brain:	n/a	n/a
22	SP1	chr5:118603605-118604819	A549	lung:	n/a	chr5:118604246-118604260
23	TEAD4	chr5:118603587-118605454	K562	blood:	n/a	n/a
24	POLR2A	chr5:118603900-118605167	GM12892	blood:	n/a	n/a
25	NFIC	chr5:118604052-118604668	HepG2	liver:	n/a	n/a
26	TAF1	chr5:118604059-118604771	SK-N-SH	brain:	n/a	n/a
27	MYC	chr5:118604179-118604629	MCF-7	breast:	n/a	n/a
28	RAD21	chr5:118603581-118605247	IMR90	lung:	n/a	chr5:118603803-118603816 chr5:118604192-118604205
29	POLR2A	chr5:118603973-118605375	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr5:118603915-118604845	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr5:118603584-118604870	GM18526	blood:	n/a	n/a
32	TBP	chr5:118603618-118605145	HepG2	liver:	n/a	n/a
33	MEF2A	chr5:118603954-118604880	GM12878	blood:	n/a	n/a
34	NR2F2	chr5:118603576-118605265	K562	blood:	n/a	n/a
35	POLR2A	chr5:118603985-118605134	K562	blood:	n/a	n/a
36	RCOR1	chr5:118604080-118605607	Hela-S3	cervix:	n/a	n/a
37	RAD21	chr5:118604058-118605184	SK-N-SH_RA	brain:	n/a	chr5:118604192-118604205
38	GABPA	chr5:118604016-118604807	K562	blood:	n/a	n/a
39	TBP	chr5:118603729-118605379	K562	blood:	n/a	n/a
40	TBL1XR1	chr5:118603900-118605240	K562	blood:	n/a	n/a
41	ELF1	chr5:118604053-118604601	HepG2	liver:	n/a	n/a
42	ELF1	chr5:118604132-118604705	K562	blood:	n/a	chr5:118604651-118604663 chr5:118604686-118604695
43	ELF1	chr5:118603580-118604637	MCF-7	breast:	n/a	n/a
44	CTCF	chr5:118604180-118604330	GM12871	blood:	n/a	n/a
45	HEY1	chr5:118604062-118604775	HepG2	liver:	n/a	chr5:118604229-118604244 chr5:118604577-118604592 chr5:118604237-118604252
46	TBL1XR1	chr5:118603743-118604616	GM12878	blood:	n/a	n/a
47	CREB1	chr5:118603544-118604573	HepG2	liver:	n/a	n/a
48	SP4	chr5:118604099-118605040	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr5:118604160-118604310	SAEC	small airway:	n/a	n/a
50	POLR2A	chr5:118603943-118604743	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:118604153..118605024-chrX:49028222..49028829,2	Hela-S3	cervix:
2	chr5:118322938..118326606-chr5:118602920..118605792,4	MCF-7	breast:
3	chr5:118406323..118408758-chr5:118602921..118606339,4	MCF-7	breast:
4	chr3:48342633..48343492-chr5:118604190..118604719,2	HCT-116	colon:
5	chr5:118323277..118326022-chr5:118603985..118605806,3	MCF-7	breast:
6	chr5:118603857..118604648-chr9:131709720..131710335,2	Hela-S3	cervix:
7	chr2:105654308..105655008-chr5:118603902..118604609,2	HCT-116	colon:
8	chr1:153508074..153508742-chr5:118604138..118604966,2	Hela-S3	cervix:

Variant related genes	Relation type
TNFAIP8	TF binding region
ENSG00000172113	Chromatin interaction
ENSG00000135972	Chromatin interaction
ENSG00000169570	Chromatin interaction
ENSG00000249494	Chromatin interaction
ENSG00000102007	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000224509	Chromatin interaction
ENSG00000095319	Chromatin interaction
ENSG00000175283	Chromatin interaction
ENSG00000172869	Chromatin interaction

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

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

rs_ID	r²[population]
rs10035593	0.84[EUR][1000 genomes]
rs10037918	0.86[EUR][1000 genomes]
rs10051559	0.84[EUR][1000 genomes]
rs10072072	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10075997	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1394628	0.89[EUR][1000 genomes]
rs1504974	0.84[EUR][1000 genomes]
rs1504975	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1504976	0.84[EUR][1000 genomes]
rs1857771	0.84[EUR][1000 genomes]
rs2271059	0.84[EUR][1000 genomes]
rs2404397	0.87[EUR][1000 genomes]
rs2896839	0.82[EUR][1000 genomes]
rs2896840	0.89[EUR][1000 genomes]
rs7736744	0.86[EUR][1000 genomes]
rs9327092	0.82[EUR][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	chr5:118603000-118606400	Active TSS	GM12878-XiMat	blood
2	chr5:118603200-118604800	Active TSS	Brain Cingulate Gyrus	brain
3	chr5:118603200-118605000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:118603200-118606600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:118603400-118604800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr5:118603400-118604800	Active TSS	Brain Anterior Caudate	brain
7	chr5:118603400-118604800	Active TSS	Colonic Mucosa	Colon
8	chr5:118603400-118605000	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr5:118603400-118605000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:118603400-118605000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:118603400-118605000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:118603400-118605000	Active TSS	Colon Smooth Muscle	Colon
13	chr5:118603400-118605000	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr5:118603400-118605000	Active TSS	NHDF-Ad	bronchial
15	chr5:118603400-118605200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:118603400-118605200	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr5:118603400-118605200	Active TSS	Psoas Muscle	Psoas
18	chr5:118603400-118605200	Active TSS	NHLF	lung
19	chr5:118603400-118605400	Active TSS	H9 Cell Line	embryonic stem cell
20	chr5:118603400-118605400	Active TSS	HSMMtube	muscle
21	chr5:118603400-118605600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:118603400-118605600	Active TSS	Brain Angular Gyrus	brain
23	chr5:118603600-118604600	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr5:118603600-118604600	Active TSS	Fetal Brain Male	brain
25	chr5:118603600-118604800	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr5:118603600-118604800	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr5:118603600-118604800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:118603600-118604800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr5:118603600-118604800	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr5:118603600-118604800	Active TSS	Fetal Muscle Trunk	muscle
31	chr5:118603600-118605000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:118603600-118605000	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr5:118603600-118605000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr5:118603600-118605000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:118603600-118605000	Active TSS	Left Ventricle	heart
36	chr5:118603600-118605000	Active TSS	Ovary	ovary
37	chr5:118603600-118605000	Active TSS	Right Atrium	heart
38	chr5:118603600-118605000	Active TSS	HMEC	breast
39	chr5:118603600-118605000	Active TSS	NH-A	brain
40	chr5:118603600-118605000	Active TSS	Osteobl	bone
41	chr5:118603600-118605200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:118603600-118605200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr5:118603600-118605200	Active TSS	Brain Hippocampus Middle	brain
44	chr5:118603600-118605200	Active TSS	Lung	lung
45	chr5:118603600-118605400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr5:118603600-118605400	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr5:118603600-118605400	Active TSS	Brain Substantia Nigra	brain
48	chr5:118603600-118605400	Active TSS	Esophagus	oesophagus
49	chr5:118603600-118605400	Active TSS	Fetal Brain Female	brain
50	chr5:118603600-118605400	Active TSS	Gastric	stomach

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