Variant report

Variant	rs55730625
Chromosome Location	chr5:43019382-43019383
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	HCFC1	chr5:43017089-43021486	Hela-S3	cervix:	n/a	n/a
2	BRCA1	chr5:43018938-43020884	Hela-S3	cervix:	n/a	n/a
3	MYC	chr5:43018990-43020788	NB4	blood:	n/a	chr5:43019739-43019748
4	MAFK	chr5:43019291-43020405	IMR90	lung:	n/a	n/a
5	TBP	chr5:43018989-43020537	GM12878	blood:	n/a	n/a
6	POLR2A	chr5:43017361-43020879	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr5:43017243-43020794	GM12878	blood:	n/a	n/a
8	FOXM1	chr5:43018983-43019566	GM12878	blood:	n/a	n/a
9	MAX	chr5:43019000-43020854	Hela-S3	cervix:	n/a	chr5:43019739-43019748
10	RCOR1	chr5:43019143-43019404	GM12878	blood:	n/a	n/a
11	GTF3C2	chr5:43018977-43020668	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr5:43018922-43020920	A549	lung:	n/a	n/a
13	CHD1	chr5:43016973-43020911	IMR90	lung:	n/a	n/a
14	MAFK	chr5:43019046-43020716	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr5:43018987-43020785	PBDE	blood:	n/a	n/a
16	POLR2A	chr5:43017338-43020832	GM19099	blood:	n/a	n/a
17	POLR2A	chr5:43019321-43019424	MCF-7	breast:	n/a	n/a
18	POLR2A	chr5:43018989-43020892	HL-60	blood:	n/a	n/a
19	MAFK	chr5:43019334-43020513	HepG2	liver:	n/a	n/a
20	CHD1	chr5:43018993-43020682	GM12878	blood:	n/a	n/a
21	SMC3	chr5:43019160-43019802	GM12878	blood:	n/a	chr5:43019704-43019711
22	POLR2A	chr5:43017296-43020789	GM12891	blood:	n/a	n/a
23	RFX5	chr5:43019017-43020796	Hela-S3	cervix:	n/a	chr5:43019166-43019182
24	CEBPB	chr5:43018967-43019386	A549	lung:	n/a	n/a
25	POLR2A	chr5:43018919-43021009	H1-neurons	neurons:	n/a	n/a
26	MXI1	chr5:43019155-43020682	GM12878	blood:	n/a	n/a
27	ZKSCAN1	chr5:43019023-43020821	Hela-S3	cervix:	n/a	n/a
28	GATA1	chr5:43018995-43020867	PBDE	blood:	n/a	chr5:43020330-43020340 chr5:43020556-43020564
29	POLR2A	chr5:43017144-43020838	GM12878	blood:	n/a	n/a
30	POLR2A	chr5:43018979-43020965	H1-neurons	neurons:	n/a	n/a
31	POLR2A	chr5:43017130-43020592	IMR90	lung:	n/a	n/a
32	GATA3	chr5:43019158-43019429	SH-SY5Y	brain:	n/a	n/a
33	TBP	chr5:43017597-43020928	Hela-S3	cervix:	n/a	n/a
34	STAT1	chr5:43018983-43020866	Hela-S3	cervix:	n/a	chr5:43020265-43020276 chr5:43020332-43020343 chr5:43020333-43020342 chr5:43020423-43020434 chr5:43020334-43020343
35	POLR2A	chr5:43017346-43020831	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr5:43017387-43020795	NB4	blood:	n/a	n/a
37	SP1	chr5:43018988-43019871	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr5:43018885-43020743	GM12878	blood:	n/a	n/a
39	SMC3	chr5:43019066-43020873	Hela-S3	cervix:	n/a	chr5:43019704-43019711
40	CEBPB	chr5:43017899-43020840	Hela-S3	cervix:	n/a	n/a
41	NFIC	chr5:43018824-43019384	GM12878	blood:	n/a	n/a
42	GATA2	chr5:43018985-43019812	HUVEC	blood vessel:	n/a	n/a
43	TBL1XR1	chr5:43019126-43019500	GM12878	blood:	n/a	n/a
44	POLR2A	chr5:43017174-43019414	HUVEC	blood vessel:	n/a	n/a
45	KAP1	chr5:43019122-43020838	HEK293	kidney:	n/a	chr5:43020162-43020170
46	CEBPB	chr5:43018968-43019461	A549	lung:	n/a	n/a
47	MAFF	chr5:43019265-43020405	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:43015093..43022227-chr5:43063428..43069370,31	MCF-7	breast:
2	chr5:40796840..40798415-chr5:43016929..43019400,2	MCF-7	breast:
3	chr5:43014739..43026335-chr5:43034830..43045515,33	MCF-7	breast:
4	chr5:43016691..43021968-chr5:43036071..43044426,17	MCF-7	breast:
5	chr5:43017018..43021813-chr5:43064660..43069370,12	MCF-7	breast:
6	chr5:43015314..43020034-chr5:43032196..43035172,5	MCF-7	breast:
7	chr5:43017490..43020535-chr5:43119535..43122363,3	MCF-7	breast:
8	chr5:42991959..42992680-chr5:43019227..43019905,2	Hela-S3	cervix:
9	chr19:36705780..36706508-chr5:43019279..43020009,2	Hela-S3	cervix:
10	chr5:43019312..43019883-chr5:43040206..43041197,3	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF131-2	chr5:43019338-43019418	ENSG00000251131.1

Variant related genes	Relation type
ENSG00000177738	TF binding region
ENSG00000196357	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000167635	Chromatin interaction
ENSG00000272382	Chromatin interaction
ENSG00000177721	Chromatin interaction
ENSG00000132356	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000215068	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1001718	1.00[AMR][1000 genomes]
rs10070393	1.00[AMR][1000 genomes]
rs28659803	1.00[AMR][1000 genomes]
rs3849700	1.00[AMR][1000 genomes]
rs60192164	1.00[AMR][1000 genomes]
rs60384612	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61328340	1.00[AMR][1000 genomes]
rs6859504	1.00[AMR][1000 genomes]
rs6860747	1.00[AMR][1000 genomes]
rs6864556	1.00[AMR][1000 genomes]
rs6869639	1.00[AMR][1000 genomes]
rs6879509	1.00[AMR][1000 genomes]
rs6881357	1.00[AMR][1000 genomes]
rs6886169	1.00[AMR][1000 genomes]
rs6887110	1.00[AMR][1000 genomes]
rs6891509	1.00[AMR][1000 genomes]
rs6891660	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6895975	1.00[AMR][1000 genomes]
rs6897663	1.00[AMR][1000 genomes]
rs73084815	1.00[AMR][1000 genomes]
rs73088862	1.00[AMR][1000 genomes]
rs73088863	1.00[AMR][1000 genomes]
rs73088878	1.00[AMR][1000 genomes]
rs73754524	1.00[AMR][1000 genomes]
rs73754532	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs747118	1.00[AMR][1000 genomes]
rs747119	1.00[AMR][1000 genomes]
rs7703982	1.00[AMR][1000 genomes]
rs7710205	1.00[AMR][1000 genomes]
rs7718462	1.00[AMR][1000 genomes]
rs7737740	1.00[AMR][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	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
8	nsv968169	chr5:42956713-43043472	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	116 gene(s)	inside rSNPs	diseases
9	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
10	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
11	nsv880447	chr5:42967215-43030798	Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
12	nsv881640	chr5:42978644-43028221	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
13	nsv880415	chr5:42978644-43030798	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	94 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	chr5:43016400-43020800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:43016800-43020800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
3	chr5:43017200-43019400	Bivalent/Poised TSS	Small Intestine	intestine
4	chr5:43017200-43020200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
5	chr5:43017200-43020600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:43017200-43020800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
7	chr5:43017400-43019400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:43017400-43019600	Active TSS	Sigmoid Colon	Sigmoid Colon
9	chr5:43017400-43019800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr5:43017400-43020000	Active TSS	Right Atrium	heart
11	chr5:43017400-43020200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
12	chr5:43017400-43020400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:43017400-43020400	Active TSS	Dnd41	blood
14	chr5:43017400-43020600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:43017400-43020600	Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr5:43017400-43020600	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr5:43017400-43020600	Bivalent/Poised TSS	Left Ventricle	heart
18	chr5:43017400-43020600	Bivalent/Poised TSS	Psoas Muscle	Psoas
19	chr5:43017400-43020600	Active TSS	Right Ventricle	heart
20	chr5:43017400-43020600	Active TSS	Thymus	Thymus
21	chr5:43017400-43020600	Active TSS	HSMMtube	muscle
22	chr5:43017400-43021400	Active TSS	A549	lung
23	chr5:43017600-43019400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:43017600-43019600	Active TSS	NHDF-Ad	bronchial
25	chr5:43017600-43019800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr5:43017600-43019800	Active TSS	NHLF	lung
27	chr5:43017600-43020200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:43017600-43020200	Bivalent/Poised TSS	Fetal Kidney	kidney
29	chr5:43017600-43020400	Active TSS	Primary monocytes fromperipheralblood	blood
30	chr5:43017600-43020400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
31	chr5:43017600-43020400	Active TSS	Monocytes-CD14+_RO01746	blood
32	chr5:43017600-43020600	Active TSS	Primary B cells from peripheral blood	blood
33	chr5:43017600-43020600	Active TSS	Primary T cells from cord blood	blood
34	chr5:43017600-43020600	Active TSS	Primary T cells fromperipheralblood	blood
35	chr5:43017600-43020600	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr5:43017600-43020600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr5:43017600-43020600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr5:43017600-43020600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr5:43017600-43020600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
40	chr5:43017600-43020600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
41	chr5:43017600-43020600	Bivalent/Poised TSS	HepG2	liver
42	chr5:43017600-43020800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:43017600-43020800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr5:43017800-43020200	Bivalent/Poised TSS	Fetal Thymus	thymus
45	chr5:43017800-43020400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:43017800-43020400	Active TSS	HUVEC	blood vessel
47	chr5:43017800-43020600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:43017800-43020600	Active TSS	GM12878-XiMat	blood
49	chr5:43018000-43019400	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr5:43018000-43019600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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