Variant report

Variant	rs10034541
Chromosome Location	chr4:87857150-87857151
allele	A/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	FOXM1	chr4:87856979-87857995	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:87857053-87857763	GM12892	blood:	n/a	n/a
3	POLR2A	chr4:87855558-87857751	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr4:87855390-87857870	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:87857126-87857641	PANC-1	pancreas:	n/a	n/a
6	JUND	chr4:87857117-87857657	Hela-S3	cervix:	n/a	chr4:87857423-87857432 chr4:87857427-87857435 chr4:87857424-87857433 chr4:87857422-87857433
7	POLR2A	chr4:87855746-87857756	GM12878	blood:	n/a	n/a
8	MYC	chr4:87857130-87857592	MCF10A-Er-Src	breast:	n/a	n/a
9	CUX1	chr4:87857125-87858337	K562	blood:	n/a	n/a
10	MAZ	chr4:87857118-87857836	HepG2	liver:	n/a	n/a
11	HEY1	chr4:87856963-87857791	HepG2	liver:	n/a	n/a
12	CEBPB	chr4:87856497-87857305	ECC-1	luminal epithelium:	n/a	n/a
13	TAF1	chr4:87856982-87857467	H1-hESC	embryonic stem cell:	n/a	n/a
14	CREB1	chr4:87856798-87857965	GM12878	blood:	n/a	n/a
15	POLR2A	chr4:87855397-87857921	GM19099	blood:	n/a	n/a
16	YY1	chr4:87856951-87857333	GM12891	blood:	n/a	n/a
17	TCF7L2	chr4:87856233-87857994	Hela-S3	cervix:	n/a	chr4:87857812-87857826 chr4:87857815-87857824 chr4:87857424-87857433
18	POLR2A	chr4:87855795-87857474	MCF-7	breast:	n/a	n/a
19	HCFC1	chr4:87855249-87857912	K562	blood:	n/a	n/a
20	ZNF143	chr4:87856572-87857437	H1-hESC	embryonic stem cell:	n/a	n/a
21	FOS	chr4:87856947-87857592	MCF10A-Er-Src	breast:	n/a	chr4:87857423-87857432 chr4:87857427-87857435 chr4:87857422-87857433 chr4:87857424-87857433
22	SMC3	chr4:87856810-87857825	Hela-S3	cervix:	n/a	n/a
23	BATF	chr4:87856994-87857773	GM12878	blood:	n/a	chr4:87857425-87857435
24	ZNF384	chr4:87857130-87858070	K562	blood:	n/a	n/a
25	SIN3A	chr4:87857054-87857961	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:87856760-87857737	HCT-116	colon:	n/a	n/a
27	POLR2A	chr4:87855314-87857869	NB4	blood:	n/a	n/a
28	CEBPB	chr4:87856536-87857732	K562	blood:	n/a	n/a
29	SP1	chr4:87857148-87857979	A549	lung:	n/a	n/a
30	POLR2A	chr4:87856064-87857845	HepG2	liver:	n/a	n/a
31	POLR2A	chr4:87855525-87857861	GM12892	blood:	n/a	n/a
32	CTCF	chr4:87857059-87857853	GM12878	blood:	n/a	n/a
33	FOS	chr4:87856952-87857607	MCF10A-Er-Src	breast:	n/a	chr4:87857423-87857432 chr4:87857427-87857435 chr4:87857422-87857433 chr4:87857424-87857433
34	MAFK	chr4:87857088-87857901	HepG2	liver:	n/a	n/a
35	POLR2A	chr4:87855410-87857773	GM12878	blood:	n/a	n/a
36	ZNF143	chr4:87856676-87857887	GM12878	blood:	n/a	n/a
37	POLR2A	chr4:87855428-87858463	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr4:87855256-87857801	K562	blood:	n/a	n/a
39	POLR2A	chr4:87856732-87857694	HCT-116	colon:	n/a	n/a
40	SMC3	chr4:87857111-87857982	GM12878	blood:	n/a	n/a
41	CEBPD	chr4:87855264-87857762	K562	blood:	n/a	n/a
42	E2F6	chr4:87856636-87857463	K562	blood:	n/a	n/a
43	CEBPB	chr4:87857084-87858012	GM12878	blood:	n/a	n/a
44	MAX	chr4:87855356-87857880	Hela-S3	cervix:	n/a	chr4:87856044-87856054 chr4:87856093-87856103
45	MBD4	chr4:87857024-87858026	HepG2	liver:	n/a	n/a
46	TAF1	chr4:87857043-87857729	K562	blood:	n/a	n/a
47	ZNF143	chr4:87856987-87857802	K562	blood:	n/a	n/a
48	CBX3	chr4:87856993-87857925	K562	blood:	n/a	n/a
49	POLR2A	chr4:87856667-87857933	HepG2	liver:	n/a	n/a
50	MYC	chr4:87855279-87858209	K562	blood:	n/a	chr4:87856044-87856054 chr4:87856093-87856103

No.	Distal block	Cell Line	Cell type
1	chr4:87855388..87857616-chr4:87927379..87929131,8	MCF-7	breast:
2	chr4:87856629..87857258-chr4:100870706..100871438,2	Hela-S3	cervix:
3	chr4:87856637..87857264-chr5:38846046..38846599,2	Hela-S3	cervix:
4	chr4:87854638..87857344-chr4:88139505..88141852,2	K562	blood:
5	chr4:87845889..87863516-chr4:87925389..87935181,79	K562	blood:
6	chr4:87855268..87857472-chr4:88140405..88143113,3	MCF-7	breast:
7	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:
8	chr4:87853395..87861870-chr4:87925425..87930611,18	MCF-7	breast:
9	chr4:87854708..87860113-chr4:87926348..87930107,23	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC10A6-2	chr4:87857140-87857330	NONHSAT097286
2	lnc-SLC10A6-2	chr4:87857140-87857320	NONHSAT097290
3	lnc-SLC10A6-2	chr4:87857140-87857354	NONHSAT097293

Variant related genes	Relation type
AFF1	TF binding region
C4orf36	TF binding region
ENSG00000172493	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000145623	Chromatin interaction
ENSG00000145332	Chromatin interaction
ENSG00000164032	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10029698	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1075989	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12186239	0.92[EUR][1000 genomes]
rs13103212	0.88[EUR][1000 genomes]
rs13112444	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13114907	0.82[EUR][1000 genomes]
rs13117826	0.88[EUR][1000 genomes]
rs13131035	0.92[EUR][1000 genomes]
rs13131194	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13134746	0.88[EUR][1000 genomes]
rs13143520	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13147942	0.88[EUR][1000 genomes]
rs13151671	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13151797	0.88[EUR][1000 genomes]
rs13434404	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2705623	0.88[EUR][1000 genomes]
rs28407685	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28439108	0.88[EUR][1000 genomes]
rs28447475	0.88[EUR][1000 genomes]
rs28457189	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28458234	0.97[EUR][1000 genomes]
rs28502831	0.92[EUR][1000 genomes]
rs28594717	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28610346	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28620528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28629974	0.92[EUR][1000 genomes]
rs28661703	0.90[EUR][1000 genomes]
rs28664715	0.92[EUR][1000 genomes]
rs28706796	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28729679	0.88[EUR][1000 genomes]
rs28854225	0.92[EUR][1000 genomes]
rs28886889	0.92[EUR][1000 genomes]
rs34077745	0.90[AMR][1000 genomes]
rs34991149	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35480728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35667731	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36053558	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71605624	0.85[EUR][1000 genomes]
rs71605686	0.88[EUR][1000 genomes]
rs71605687	0.88[EUR][1000 genomes]
rs71605688	0.92[EUR][1000 genomes]
rs71605691	0.94[EUR][1000 genomes]
rs71605693	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7683045	0.88[EUR][1000 genomes]
rs9993812	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9999001	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	esv3421759	chr4:87855153-87857701	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr4:87854800-87858600	Active TSS	Right Ventricle	heart
2	chr4:87854800-87859200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:87855000-87857400	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr4:87855000-87857400	Active TSS	Aorta	Aorta
5	chr4:87855000-87857400	Active TSS	HSMMtube	muscle
6	chr4:87855000-87857800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:87855000-87857800	Active TSS	Brain Angular Gyrus	brain
8	chr4:87855000-87858000	Active TSS	Duodenum Mucosa	Duodenum
9	chr4:87855000-87858000	Active TSS	HMEC	breast
10	chr4:87855000-87858200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr4:87855000-87858400	Active TSS	H9 Cell Line	embryonic stem cell
12	chr4:87855000-87858400	Active TSS	Psoas Muscle	Psoas
13	chr4:87855000-87859000	Active TSS	Colonic Mucosa	Colon
14	chr4:87855000-87859000	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr4:87855000-87859800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:87855200-87857200	Active TSS	Fetal Intestine Small	intestine
17	chr4:87855200-87857400	Active TSS	Fetal Heart	heart
18	chr4:87855200-87857600	Active TSS	Colon Smooth Muscle	Colon
19	chr4:87855200-87857600	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr4:87855200-87857600	Active TSS	NHDF-Ad	bronchial
21	chr4:87855200-87857800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:87855200-87857800	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr4:87855200-87857800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:87855200-87857800	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr4:87855200-87857800	Active TSS	Left Ventricle	heart
26	chr4:87855200-87857800	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr4:87855200-87858200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:87855200-87858200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:87855200-87858200	Active TSS	Brain Hippocampus Middle	brain
30	chr4:87855200-87858200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:87855200-87858200	Active TSS	A549	lung
32	chr4:87855200-87858400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:87855200-87858400	Active TSS	Placenta Amnion	Placenta Amnion
34	chr4:87855200-87858600	Active TSS	Stomach Mucosa	stomach
35	chr4:87855200-87859000	Active TSS	Fetal Intestine Large	intestine
36	chr4:87855200-87859200	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr4:87855200-87859200	Active TSS	H1 Cell Line	embryonic stem cell
38	chr4:87855200-87859800	Active TSS	GM12878-XiMat	blood
39	chr4:87855200-87859800	Active TSS	Hela-S3	cervix
40	chr4:87855400-87857200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:87855400-87857600	Active TSS	Small Intestine	intestine
42	chr4:87855400-87857800	Active TSS	Esophagus	oesophagus
43	chr4:87855400-87857800	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr4:87855400-87857800	Active TSS	Gastric	stomach
45	chr4:87855400-87857800	Active TSS	Lung	lung
46	chr4:87855400-87857800	Active TSS	Pancreas	Pancrea
47	chr4:87855400-87858000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr4:87855400-87858000	Active TSS	Rectal Smooth Muscle	rectum
49	chr4:87855400-87858200	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr4:87855400-87858200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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