Variant report

Variant	rs316409
Chromosome Location	chr5:43065469-43065470
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:153)
CpG islands
(count:0)
Chromatin interactive
region (count:35)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:153 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:43064625-43065491	MCF-7	breast:	n/a	n/a
2	SMC3	chr5:43064843-43065679	Hela-S3	cervix:	n/a	n/a
3	CHD1	chr5:43064893-43067580	GM12878	blood:	n/a	n/a
4	POLR2A	chr5:43063699-43068095	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr5:43064871-43065633	Hela-S3	cervix:	n/a	n/a
6	KAP1	chr5:43064995-43065606	K562	blood:	n/a	n/a
7	CTCF	chr5:43064553-43067516	SK-N-SH	brain:	n/a	chr5:43065140-43065149
8	POLR2A	chr5:43064657-43068004	GM12878	blood:	n/a	n/a
9	CTCF	chr5:43064893-43065485	MCF-7	breast:	n/a	chr5:43065140-43065149
10	POLR2A	chr5:43064721-43068001	GM12878	blood:	n/a	n/a
11	FOSL2	chr5:43064663-43065670	A549	lung:	n/a	chr5:43065126-43065140
12	MAX	chr5:43064743-43067718	Hela-S3	cervix:	n/a	chr5:43066604-43066614
13	POLR2A	chr5:43065384-43066103	U87	brain:	n/a	n/a
14	MYC	chr5:43064704-43067504	K562	blood:	n/a	chr5:43066604-43066614
15	MXI1	chr5:43064468-43068129	SK-N-SH	brain:	n/a	n/a
16	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
17	POLR2A	chr5:43064633-43067996	K562	blood:	n/a	n/a
18	POLR2A	chr5:43065425-43065810	K562	blood:	n/a	n/a
19	POLR2A	chr5:43065414-43068014	PANC-1	pancreas:	n/a	n/a
20	MXI1	chr5:43064802-43065566	GM12878	blood:	n/a	n/a
21	POLR2A	chr5:43064544-43068001	K562	blood:	n/a	n/a
22	GABPA	chr5:43064772-43065528	MCF-7	breast:	n/a	n/a
23	TRIM28	chr5:43064563-43067621	K562	blood:	n/a	n/a
24	POLR2A	chr5:43065412-43067928	GM12892	blood:	n/a	n/a
25	CUX1	chr5:43064824-43065591	GM12878	blood:	n/a	n/a
26	TAF1	chr5:43065401-43067715	A549	lung:	n/a	n/a
27	TCF12	chr5:43064736-43065540	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr5:43064658-43065712	HUVEC	blood vessel:	n/a	n/a
29	GATA1	chr5:43064680-43065842	PBDE	blood:	n/a	n/a
30	YY1	chr5:43065451-43065723	A549	lung:	n/a	n/a
31	POLR2A	chr5:43064700-43067893	HUVEC	blood vessel:	n/a	n/a
32	PML	chr5:43064692-43065888	K562	blood:	n/a	n/a
33	RCOR1	chr5:43064562-43065695	K562	blood:	n/a	n/a
34	POLR2A	chr5:43064529-43067905	HL-60	blood:	n/a	n/a
35	TCF12	chr5:43063710-43067869	A549	lung:	n/a	n/a
36	BRCA1	chr5:43064827-43066009	Hela-S3	cervix:	n/a	n/a
37	GTF2F1	chr5:43064788-43068150	Hela-S3	cervix:	n/a	n/a
38	CTCF	chr5:43064883-43065601	IMR90	lung:	n/a	chr5:43065140-43065149
39	POLR2A	chr5:43064656-43067965	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr5:43064554-43068184	SK-N-MC	brain:	n/a	n/a
41	MAFF	chr5:43064858-43065681	HepG2	liver:	n/a	n/a
42	MAX	chr5:43064660-43067825	Hela-S3	cervix:	n/a	chr5:43066604-43066614
43	TBL1XR1	chr5:43064811-43065793	K562	blood:	n/a	n/a
44	POLR2A	chr5:43063968-43067900	K562	blood:	n/a	n/a
45	MYC	chr5:43064705-43068115	K562	blood:	n/a	chr5:43066604-43066614
46	REST	chr5:43064738-43067687	A549	lung:	n/a	chr5:43067604-43067617 chr5:43066994-43067008 chr5:43066605-43066618
47	POLR2A	chr5:43064666-43067951	K562	blood:	n/a	n/a
48	POLR2A	chr5:43064728-43067783	HepG2	liver:	n/a	n/a
49	POLR2A	chr5:43064690-43067878	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr5:43063423-43067967	PANC-1	pancreas:	n/a	n/a

No data

(count:35 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43062770..43067811-chr5:43482181..43486392,9	K562	blood:
2	chr5:43062052..43069089-chr5:43119705..43123366,12	MCF-7	breast:
3	chr5:42907010..42910562-chr5:43064999..43067630,3	MCF-7	breast:
4	chr5:43064995..43071284-chr5:43119667..43123996,15	MCF-7	breast:
5	chr5:43063931..43068016-chr5:43554200..43557480,3	K562	blood:
6	chr5:43037720..43044659-chr5:43062293..43069444,31	K562	blood:
7	chr17:21187752..21188425-chr5:43065158..43065907,2	Hela-S3	cervix:
8	chr5:43017018..43021813-chr5:43064660..43069370,12	MCF-7	breast:
9	chr5:43065277..43067135-chr5:43287276..43290196,2	K562	blood:
10	chr5:43063463..43067998-chr5:43119333..43125586,12	K562	blood:
11	chr5:43038662..43048059-chr5:43059399..43070773,40	MCF-7	breast:
12	chr11:62608627..62609498-chr5:43065084..43065931,2	NB4	blood:
13	chr5:42907363..42912501-chr5:43064737..43069149,8	MCF-7	breast:
14	chr5:43064382..43066342-chr5:43482298..43484520,2	MCF-7	breast:
15	chr5:43006860..43010287-chr5:43063692..43067440,8	K562	blood:
16	chr20:39656786..39657534-chr5:43064705..43065538,2	NB4	blood:
17	chr5:43064858..43068068-chr5:43482667..43486392,7	K562	blood:
18	chr5:43036901..43050217-chr5:43060442..43069391,53	MCF-7	breast:
19	chr5:43005189..43014948-chr5:43062554..43069130,17	MCF-7	breast:
20	chr20:32699690..32700555-chr5:43064843..43065502,2	Hela-S3	cervix:
21	chr12:52449523..52450198-chr5:43065183..43066078,2	Hela-S3	cervix:
22	chr5:43063723..43068505-chr5:43119531..43125230,17	K562	blood:
23	chr17:49021660..49022269-chr5:43064578..43065548,2	Hela-S3	cervix:
24	chr1:201923958..201924913-chr5:43065138..43065692,2	Hela-S3	cervix:
25	chr5:43006765..43010626-chr5:43063692..43068627,9	K562	blood:
26	chr5:43041320..43043003-chr5:43064736..43065650,5	MCF-7	breast:
27	chr5:43015093..43022227-chr5:43063428..43069370,31	MCF-7	breast:
28	chr5:43041236..43041956-chr5:43064471..43065638,4	K562	blood:
29	chr3:150263846..150264359-chr5:43065322..43065951,2	Hela-S3	cervix:
30	chr5:41924171..41926713-chr5:43064683..43066902,2	K562	blood:
31	chr5:43061295..43063286-chr5:43064759..43067146,4	MCF-7	breast:
32	chr5:43064535..43068771-chr5:43312463..43314872,5	MCF-7	breast:
33	chr17:38473520..38475721-chr5:43065079..43067776,2	MCF-7	breast:
34	chr5:43006162..43011722-chr5:43063736..43068779,9	MCF-7	breast:
35	chr5:43034726..43053192-chr5:43061725..43074206,66	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC114947.1.1-2	chr5:43065261-43067736	XLOC_004366
2	lnc-C5orf39-1	chr5:43065289-43067073	NONHSAT101276

No data

Variant related genes	Relation type
ZNF131	TF binding region
ENSG00000172239	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000177721	Chromatin interaction
ENSG00000151881	Chromatin interaction
ENSG00000120742	Chromatin interaction
ENSG00000198900	Chromatin interaction
ENSG00000251656	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000261604	Chromatin interaction
ENSG00000151876	Chromatin interaction
ENSG00000247011	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000125977	Chromatin interaction
ENSG00000251131	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000134375	Chromatin interaction
ENSG00000112972	Chromatin interaction
ENSG00000034152	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000271788	Chromatin interaction
ENSG00000215068	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000272144	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1032434	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10454865	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10941607	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10941608	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11550285	0.92[ASN][1000 genomes]
rs11550286	0.93[ASN][1000 genomes]
rs11550287	0.93[ASN][1000 genomes]
rs11740797	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11742691	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11743246	0.80[ASN][1000 genomes]
rs11747015	0.80[AMR][1000 genomes]
rs11748187	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750239	0.81[ASN][1000 genomes]
rs11949817	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11954543	0.80[ASN][1000 genomes]
rs11956243	0.93[ASN][1000 genomes]
rs12188691	0.82[ASN][1000 genomes]
rs13155513	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13159703	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13165504	0.82[ASN][1000 genomes]
rs13169563	0.98[ASN][1000 genomes]
rs13173064	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17301375	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2452831	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316398	0.82[ASN][1000 genomes]
rs316405	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316410	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316411	0.91[ASN][1000 genomes]
rs316418	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3207358	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34087147	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34315422	0.95[ASN][1000 genomes]
rs34492794	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34670023	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34808919	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34859360	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35085573	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35541316	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36039989	0.93[ASN][1000 genomes]
rs36083302	0.95[ASN][1000 genomes]
rs3733839	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797312	0.80[ASN][1000 genomes]
rs3849698	0.80[ASN][1000 genomes]
rs3849699	0.82[ASN][1000 genomes]
rs493097	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504404	0.88[ASN][1000 genomes]
rs55939188	0.83[AMR][1000 genomes]
rs56169202	0.82[ASN][1000 genomes]
rs581914	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62367685	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62367688	0.96[ASN][1000 genomes]
rs62372869	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs670206	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6864223	0.93[ASN][1000 genomes]
rs7709181	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7729529	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9790935	0.80[AMR][1000 genomes];0.82[ASN][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	chr5:43045400-43066000	Weak transcription	Spleen	Spleen
2	chr5:43063600-43068200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:43063800-43068200	Active TSS	A549	lung
4	chr5:43064000-43067800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr5:43064000-43068000	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr5:43064000-43068400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:43064200-43068200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr5:43064200-43068200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:43064200-43068400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr5:43064200-43069000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:43064400-43066000	Active TSS	Brain Germinal Matrix	brain
12	chr5:43064400-43067200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:43064400-43067400	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr5:43064400-43067600	Active TSS	Brain Hippocampus Middle	brain
15	chr5:43064400-43067600	Active TSS	Brain Substantia Nigra	brain
16	chr5:43064400-43067600	Active TSS	Colonic Mucosa	Colon
17	chr5:43064400-43067800	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr5:43064400-43067800	Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr5:43064400-43067800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:43064400-43067800	Active TSS	Brain Cingulate Gyrus	brain
21	chr5:43064400-43067800	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr5:43064400-43067800	Active TSS	Fetal Brain Female	brain
23	chr5:43064400-43067800	Active TSS	Fetal Intestine Large	intestine
24	chr5:43064400-43067800	Active TSS	Fetal Lung	lung
25	chr5:43064400-43067800	Active TSS	Thymus	Thymus
26	chr5:43064400-43068000	Active TSS	Esophagus	oesophagus
27	chr5:43064400-43068000	Active TSS	Fetal Kidney	kidney
28	chr5:43064400-43068000	Active TSS	Fetal Stomach	stomach
29	chr5:43064400-43068000	Active TSS	Rectal Smooth Muscle	rectum
30	chr5:43064400-43068000	Active TSS	Stomach Smooth Muscle	stomach
31	chr5:43064400-43068200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:43064400-43068200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:43064400-43068200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:43064400-43068200	Active TSS	Psoas Muscle	Psoas
35	chr5:43064400-43068200	Active TSS	Right Ventricle	heart
36	chr5:43064400-43068400	Active TSS	NHDF-Ad	bronchial
37	chr5:43064600-43066800	Active TSS	Right Atrium	heart
38	chr5:43064600-43067400	ZNF genes & repeats	Fetal Brain Male	brain
39	chr5:43064600-43067600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr5:43064600-43067600	Active TSS	Brain Angular Gyrus	brain
41	chr5:43064600-43067600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr5:43064600-43067800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:43064600-43067800	Active TSS	Brain Anterior Caudate	brain
44	chr5:43064600-43067800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:43064600-43068000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr5:43064600-43068000	Active TSS	Colon Smooth Muscle	Colon
47	chr5:43064600-43068000	Active TSS	Small Intestine	intestine
48	chr5:43064600-43068000	Active TSS	Stomach Mucosa	stomach
49	chr5:43064600-43068200	Active TSS	Gastric	stomach
50	chr5:43064600-43068200	Active TSS	Ovary	ovary

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