Variant report

Variant	rs6883407
Chromosome Location	chr5:43066265-43066266
allele	A/C/G/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	chr5:43065943-43067771	H1-hESC	embryonic stem cell:	n/a	n/a
2	EBF1	chr5:43066254-43066673	GM12878	blood:	n/a	n/a
3	EBF1	chr5:43066217-43066603	GM12878	blood:	n/a	n/a
4	SMARCC1	chr5:43065831-43068011	Hela-S3	cervix:	n/a	n/a
5	CHD1	chr5:43064893-43067580	GM12878	blood:	n/a	n/a
6	BHLHE40	chr5:43065837-43067282	GM12878	blood:	n/a	n/a
7	POLR2A	chr5:43063699-43068095	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr5:43065794-43067439	HepG2	liver:	n/a	chr5:43066604-43066614
9	MAX	chr5:43065693-43067951	A549	lung:	n/a	chr5:43066604-43066614
10	POLR2A	chr5:43066206-43066809	K562	blood:	n/a	n/a
11	HMGN3	chr5:43066005-43067410	K562	blood:	n/a	n/a
12	SMARCB1	chr5:43065917-43067848	Hela-S3	cervix:	n/a	n/a
13	RUNX3	chr5:43065496-43067460	GM12878	blood:	n/a	n/a
14	ELF1	chr5:43066254-43066744	K562	blood:	n/a	chr5:43066484-43066493 chr5:43066690-43066699
15	BCLAF1	chr5:43065861-43067383	GM12878	blood:	n/a	chr5:43066480-43066493 chr5:43066792-43066805
16	CTCF	chr5:43064553-43067516	SK-N-SH	brain:	n/a	chr5:43065140-43065149
17	POLR2A	chr5:43064657-43068004	GM12878	blood:	n/a	n/a
18	JUN	chr5:43066243-43067269	K562	blood:	n/a	n/a
19	POLR2A	chr5:43064721-43068001	GM12878	blood:	n/a	n/a
20	POLR2A	chr5:43065769-43067766	GM12892	blood:	n/a	n/a
21	MAX	chr5:43065907-43068007	K562	blood:	n/a	chr5:43066604-43066614
22	TAF7	chr5:43066234-43067331	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr5:43064743-43067718	Hela-S3	cervix:	n/a	chr5:43066604-43066614
24	E2F6	chr5:43065951-43067789	K562	blood:	n/a	chr5:43066826-43066833
25	POLR2A	chr5:43066092-43067773	H1-hESC	embryonic stem cell:	n/a	n/a
26	MYC	chr5:43064704-43067504	K562	blood:	n/a	chr5:43066604-43066614
27	POLR2A	chr5:43065507-43067802	MCF-7	breast:	n/a	n/a
28	MXI1	chr5:43064468-43068129	SK-N-SH	brain:	n/a	n/a
29	SIN3AK20	chr5:43065869-43067496	PANC-1	pancreas:	n/a	n/a
30	YY1	chr5:43064825-43067985	SK-N-SH	brain:	n/a	chr5:43066704-43066716 chr5:43066481-43066490 chr5:43066761-43066771 chr5:43066694-43066716 chr5:43066706-43066716
31	HCFC1	chr5:43066200-43067731	K562	blood:	n/a	n/a
32	POLR2A	chr5:43064633-43067996	K562	blood:	n/a	n/a
33	POLR2A	chr5:43065414-43068014	PANC-1	pancreas:	n/a	n/a
34	YY1	chr5:43065845-43067406	GM12878	blood:	n/a	chr5:43066704-43066716 chr5:43066481-43066490 chr5:43066761-43066771 chr5:43066694-43066716 chr5:43066706-43066716
35	YY1	chr5:43066203-43067522	SK-N-SH_RA	brain:	n/a	chr5:43066704-43066716 chr5:43066481-43066490 chr5:43066761-43066771 chr5:43066694-43066716 chr5:43066706-43066716
36	POLR2A	chr5:43065754-43067323	PFSK-1	brain:	n/a	n/a
37	SETDB1	chr5:43066007-43067673	K562	blood:	n/a	chr5:43067636-43067660
38	POLR2A	chr5:43064544-43068001	K562	blood:	n/a	n/a
39	POLR2A	chr5:43065774-43067874	GM12892	blood:	n/a	n/a
40	CHD2	chr5:43066220-43067278	K562	blood:	n/a	n/a
41	TEAD4	chr5:43065999-43067305	ECC-1	luminal epithelium:	n/a	n/a
42	EP300	chr5:43066240-43067922	GM12878	blood:	n/a	chr5:43066928-43066944 chr5:43066605-43066621 chr5:43066932-43066948 chr5:43066481-43066490 chr5:43066482-43066491
43	YY1	chr5:43065821-43067599	A549	lung:	n/a	chr5:43066704-43066716 chr5:43066481-43066490 chr5:43066761-43066771 chr5:43066694-43066716 chr5:43066706-43066716
44	CTCF	chr5:43066180-43066330	HCPEpiC	choroid plexus:	n/a	n/a
45	GATA1	chr5:43066061-43067795	PBDE	blood:	n/a	n/a
46	POLR2A	chr5:43065985-43067717	MCF-7	breast:	n/a	n/a
47	TRIM28	chr5:43064563-43067621	K562	blood:	n/a	n/a
48	POLR2A	chr5:43065412-43067928	GM12892	blood:	n/a	n/a
49	TAF1	chr5:43065401-43067715	A549	lung:	n/a	n/a
50	YY1	chr5:43065803-43067367	GM12891	blood:	n/a	chr5:43066704-43066716 chr5:43066481-43066490 chr5:43066761-43066771 chr5:43066694-43066716 chr5:43066706-43066716

No.	Distal block	Cell Line	Cell type
1	chr5:43065577..43067489-chr5:43555755..43557297,2	K562	blood:
2	chr5:43062770..43067811-chr5:43482181..43486392,9	K562	blood:
3	chr5:43062052..43069089-chr5:43119705..43123366,12	MCF-7	breast:
4	chr5:42907010..42910562-chr5:43064999..43067630,3	MCF-7	breast:
5	chr5:43064995..43071284-chr5:43119667..43123996,15	MCF-7	breast:
6	chr5:43026063..43028534-chr5:43065548..43067073,2	MCF-7	breast:
7	chr5:43063931..43068016-chr5:43554200..43557480,3	K562	blood:
8	chr5:43037720..43044659-chr5:43062293..43069444,31	K562	blood:
9	chr5:42927540..42930001-chr5:43065778..43067450,2	MCF-7	breast:
10	chr5:43017018..43021813-chr5:43064660..43069370,12	MCF-7	breast:
11	chr5:43065277..43067135-chr5:43287276..43290196,2	K562	blood:
12	chr5:43065921..43066620-chr6:2765473..2766156,2	Hela-S3	cervix:
13	chr11:35965082..35965951-chr5:43065901..43066524,2	Hela-S3	cervix:
14	chr5:43063463..43067998-chr5:43119333..43125586,12	K562	blood:
15	chr5:43038662..43048059-chr5:43059399..43070773,40	MCF-7	breast:
16	chr5:42907363..42912501-chr5:43064737..43069149,8	MCF-7	breast:
17	chr5:43064382..43066342-chr5:43482298..43484520,2	MCF-7	breast:
18	chr5:43006860..43010287-chr5:43063692..43067440,8	K562	blood:
19	chr11:62608827..62609716-chr5:43065667..43066332,2	Hela-S3	cervix:
20	chr5:43066182..43066736-chr9:111881958..111882554,2	Hela-S3	cervix:
21	chr20:49347801..49350191-chr5:43066077..43068758,2	MCF-7	breast:
22	chr5:43064858..43068068-chr5:43482667..43486392,7	K562	blood:
23	chr5:43036901..43050217-chr5:43060442..43069391,53	MCF-7	breast:
24	chr5:43005189..43014948-chr5:43062554..43069130,17	MCF-7	breast:
25	chr5:43063723..43068505-chr5:43119531..43125230,17	K562	blood:
26	chr5:43065851..43066733-chr5:177631101..177631947,2	Hela-S3	cervix:
27	chr5:43006765..43010626-chr5:43063692..43068627,9	K562	blood:
28	chr5:43065667..43066298-chr5:43483878..43484622,3	Hela-S3	cervix:
29	chr5:43015093..43022227-chr5:43063428..43069370,31	MCF-7	breast:
30	chr19:13274236..13274884-chr5:43065745..43066308,2	Hela-S3	cervix:
31	chr5:41924171..41926713-chr5:43064683..43066902,2	K562	blood:
32	chr5:43061295..43063286-chr5:43064759..43067146,4	MCF-7	breast:
33	chr5:43065608..43069318-chr5:43481836..43485606,6	MCF-7	breast:
34	chr5:43064535..43068771-chr5:43312463..43314872,5	MCF-7	breast:
35	chr17:38473520..38475721-chr5:43065079..43067776,2	MCF-7	breast:
36	chr5:43006162..43011722-chr5:43063736..43068779,9	MCF-7	breast:
37	chr17:47268969..47269922-chr5:43065803..43066617,2	Hela-S3	cervix:
38	chr5:43034726..43053192-chr5:43061725..43074206,66	K562	blood:
39	chr11:67777806..67778578-chr5:43066246..43066840,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC114947.1.1-2	chr5:43065761-43067736	XLOC_004366
2	lnc-AC114947.1.1-2	chr5:43066192-43067888	XLOC_004366
3	lnc-AC114947.1.1-2	chr5:43065261-43067736	XLOC_004366
4	lnc-AC114947.1.1-2	chr5:43066235-43067736	XLOC_004366
5	lnc-AC114947.1.1-2	chr5:43066191-43067736	XLOC_004366
6	lnc-C5orf39-1	chr5:43065289-43067073	NONHSAT101276

Variant related genes	Relation type
ZNF131	TF binding region
ENSG00000133316	Chromatin interaction
ENSG00000271788	Chromatin interaction
ENSG00000177721	Chromatin interaction
ENSG00000261604	Chromatin interaction
ENSG00000151881	Chromatin interaction
ENSG00000251656	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000124535	Chromatin interaction
ENSG00000006534	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000172239	Chromatin interaction
ENSG00000272144	Chromatin interaction
ENSG00000151876	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000179241	Chromatin interaction
ENSG00000112972	Chromatin interaction
ENSG00000197451	Chromatin interaction
ENSG00000106771	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000215068	Chromatin interaction
ENSG00000251131	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10805669	1.00[AMR][1000 genomes]
rs10971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16872916	1.00[AMR][1000 genomes]
rs1690990	1.00[AMR][1000 genomes]
rs4473775	1.00[AMR][1000 genomes]
rs4533896	1.00[AMR][1000 genomes]
rs4588602	1.00[AMR][1000 genomes]
rs4637561	1.00[AMR][1000 genomes]
rs634129	1.00[AMR][1000 genomes]
rs6451679	1.00[AMR][1000 genomes]
rs6859969	1.00[AMR][1000 genomes]
rs6868271	1.00[AMR][1000 genomes]
rs6868325	1.00[AMR][1000 genomes]
rs6880391	1.00[AMR][1000 genomes]
rs7700263	1.00[AFR][1000 genomes]
rs7702457	1.00[AMR][1000 genomes]
rs7705935	1.00[AMR][1000 genomes]
rs7726407	1.00[AMR][1000 genomes]
rs782992	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
8	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
9	nsv870299	chr5:43053679-43107880	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	68 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	chr5:43063600-43068200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr5:43063800-43068200	Active TSS	A549	lung
3	chr5:43064000-43067800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr5:43064000-43068000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr5:43064000-43068400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:43064200-43068200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr5:43064200-43068200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:43064200-43068400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr5:43064200-43069000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:43064400-43067200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:43064400-43067400	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr5:43064400-43067600	Active TSS	Brain Hippocampus Middle	brain
13	chr5:43064400-43067600	Active TSS	Brain Substantia Nigra	brain
14	chr5:43064400-43067600	Active TSS	Colonic Mucosa	Colon
15	chr5:43064400-43067800	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr5:43064400-43067800	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr5:43064400-43067800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:43064400-43067800	Active TSS	Brain Cingulate Gyrus	brain
19	chr5:43064400-43067800	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr5:43064400-43067800	Active TSS	Fetal Brain Female	brain
21	chr5:43064400-43067800	Active TSS	Fetal Intestine Large	intestine
22	chr5:43064400-43067800	Active TSS	Fetal Lung	lung
23	chr5:43064400-43067800	Active TSS	Thymus	Thymus
24	chr5:43064400-43068000	Active TSS	Esophagus	oesophagus
25	chr5:43064400-43068000	Active TSS	Fetal Kidney	kidney
26	chr5:43064400-43068000	Active TSS	Fetal Stomach	stomach
27	chr5:43064400-43068000	Active TSS	Rectal Smooth Muscle	rectum
28	chr5:43064400-43068000	Active TSS	Stomach Smooth Muscle	stomach
29	chr5:43064400-43068200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:43064400-43068200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:43064400-43068200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:43064400-43068200	Active TSS	Psoas Muscle	Psoas
33	chr5:43064400-43068200	Active TSS	Right Ventricle	heart
34	chr5:43064400-43068400	Active TSS	NHDF-Ad	bronchial
35	chr5:43064600-43066800	Active TSS	Right Atrium	heart
36	chr5:43064600-43067400	ZNF genes & repeats	Fetal Brain Male	brain
37	chr5:43064600-43067600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:43064600-43067600	Active TSS	Brain Angular Gyrus	brain
39	chr5:43064600-43067600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr5:43064600-43067800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:43064600-43067800	Active TSS	Brain Anterior Caudate	brain
42	chr5:43064600-43067800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr5:43064600-43068000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:43064600-43068000	Active TSS	Colon Smooth Muscle	Colon
45	chr5:43064600-43068000	Active TSS	Small Intestine	intestine
46	chr5:43064600-43068000	Active TSS	Stomach Mucosa	stomach
47	chr5:43064600-43068200	Active TSS	Gastric	stomach
48	chr5:43064600-43068200	Active TSS	Ovary	ovary
49	chr5:43064600-43068200	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr5:43064600-43068400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links