Variant report

Variant	rs4727771
Chromosome Location	chr7:112092347-112092348
allele	C/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	JUND	chr7:112092310-112092901	K562	blood:	n/a	n/a
2	POLR2A	chr7:112092054-112092521	U87	brain:	n/a	n/a
3	POLR2A	chr7:112092151-112092571	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:112089968-112092839	IMR90	lung:	n/a	n/a
5	POLR2A	chr7:112091789-112092647	Hela-S3	cervix:	n/a	n/a
6	MAX	chr7:112092191-112092855	NB4	blood:	n/a	chr7:112092799-112092808
7	POLR2A	chr7:112089448-112092907	HepG2	liver:	n/a	n/a
8	POLR2A	chr7:112092229-112092388	MCF-7	breast:	n/a	n/a
9	CHD1	chr7:112090507-112093089	H1-hESC	embryonic stem cell:	n/a	chr7:112091005-112091015
10	REST	chr7:112089562-112092667	H1-neurons	neurons:	n/a	chr7:112092117-112092137 chr7:112091534-112091554 chr7:112090684-112090702 chr7:112091540-112091554
11	POLR2A	chr7:112092073-112092521	U87	brain:	n/a	n/a
12	RCOR1	chr7:112092313-112092846	GM12878	blood:	n/a	n/a
13	SMC3	chr7:112092317-112092364	GM12878	blood:	n/a	n/a
14	MXI1	chr7:112092277-112092468	Hela-S3	cervix:	n/a	n/a
15	CCNT2	chr7:112092100-112092474	K562	blood:	n/a	n/a
16	CTCF	chr7:112092220-112092370	HFF-Myc	foreskin:	n/a	n/a
17	MXI1	chr7:112089314-112092845	IMR90	lung:	n/a	chr7:112091383-112091392 chr7:112090466-112090475
18	USF1	chr7:112092269-112092555	SK-N-SH_RA	brain:	n/a	chr7:112092357-112092368
19	MYC	chr7:112092211-112092742	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZC3H11A	chr7:112092321-112092900	K562	blood:	n/a	n/a
21	POLR2A	chr7:112092147-112092838	GM12878	blood:	n/a	n/a
22	POLR2A	chr7:112092069-112092504	H1-neurons	neurons:	n/a	n/a
23	USF1	chr7:112092197-112092571	K562	blood:	n/a	chr7:112092357-112092368
24	UBTF	chr7:112092258-112092899	K562	blood:	n/a	n/a
25	WRNIP1	chr7:112091913-112092459	GM12878	blood:	n/a	n/a
26	UBTF	chr7:112092198-112092493	K562	blood:	n/a	n/a
27	USF1	chr7:112092258-112092520	HepG2	liver:	n/a	chr7:112092357-112092368
28	ZNF384	chr7:112091652-112092571	K562	blood:	n/a	n/a
29	TBP	chr7:112092253-112092826	H1-hESC	embryonic stem cell:	n/a	n/a
30	NR2F2	chr7:112089740-112093055	K562	blood:	n/a	chr7:112092790-112092805
31	GTF2F1	chr7:112092264-112092368	Hela-S3	cervix:	n/a	n/a
32	USF1	chr7:112092256-112092538	SK-N-SH_RA	brain:	n/a	chr7:112092357-112092368
33	POLR2A	chr7:112089647-112092731	Hela-S3	cervix:	n/a	n/a
34	TBL1XR1	chr7:112092310-112092546	K562	blood:	n/a	n/a
35	CHD2	chr7:112092272-112092473	K562	blood:	n/a	n/a
36	POLR2A	chr7:112092166-112092519	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr7:112089828-112092544	PBDE	blood:	n/a	n/a
38	MAX	chr7:112092273-112092834	Hela-S3	cervix:	n/a	chr7:112092799-112092808
39	POLR2A	chr7:112092107-112092500	K562	blood:	n/a	n/a
40	BHLHE40	chr7:112092024-112092781	K562	blood:	n/a	n/a
41	ZNF263	chr7:112089981-112092890	HEK293-T-REx	kidney:	n/a	chr7:112090268-112090277 chr7:112092703-112092712
42	EBF1	chr7:112092263-112092862	GM12878	blood:	n/a	chr7:112092440-112092451
43	POLR2A	chr7:112092093-112092559	H1-hESC	embryonic stem cell:	n/a	n/a
44	GATA1	chr7:112089986-112092410	PBDE	blood:	n/a	chr7:112090961-112090969
45	POLR2A	chr7:112092177-112092520	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr7:112092166-112092572	K562	blood:	n/a	n/a
47	ARID3A	chr7:112092070-112093011	HepG2	liver:	n/a	n/a
48	POLR2A	chr7:112090070-112093219	K562	blood:	n/a	n/a
49	POLR2A	chr7:112089306-112092632	MCF10A-Er-Src	breast:	n/a	n/a
50	TBL1XR1	chr7:112092224-112092902	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:111977606..111981678-chr7:112089523..112092927,4	K562	blood:
2	chr7:112088943..112098465-chr7:112111106..112127214,31	K562	blood:
3	chr7:108208069..108211100-chr7:112089167..112092388,3	K562	blood:
4	chr7:112089471..112094125-chr7:112120459..112123941,5	MCF-7	breast:
5	chr7:112088811..112094041-chr7:112100770..112110657,18	MCF-7	breast:
6	chr7:112088410..112092985-chr7:112428999..112431698,4	K562	blood:
7	chr7:112047884..112050486-chr7:112089235..112093334,4	MCF-7	breast:
8	chr7:112089375..112094700-chr7:112096975..112100569,9	MCF-7	breast:
9	chr7:112048671..112054554-chr7:112088966..112092653,8	K562	blood:
10	chr7:112059129..112067568-chr7:112088387..112093703,18	K562	blood:
11	chr1:24968714..24969624-chr7:112092230..112092922,2	Hela-S3	cervix:
12	chr7:112058803..112077296-chr7:112087519..112096464,50	MCF-7	breast:
13	chr7:112058693..112068099-chr7:112086961..112092875,22	MCF-7	breast:
14	chr7:112060645..112065287-chr7:112088150..112093147,11	K562	blood:
15	chr7:111986864..111991026-chr7:112090313..112092457,3	MCF-7	breast:
16	chr7:108209600..108213665-chr7:112090307..112092525,3	K562	blood:

Variant related genes	Relation type
IFRD1	TF binding region
ENSG00000146802	Chromatin interaction
ENSG00000133226	Chromatin interaction
ENSG00000198839	Chromatin interaction
ENSG00000177683	Chromatin interaction
ENSG00000181016	Chromatin interaction
ENSG00000006652	Chromatin interaction
ENSG00000226851	Chromatin interaction
ENSG00000128590	Chromatin interaction
ENSG00000135241	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1005659	0.91[ASN][1000 genomes]
rs1005661	0.91[ASN][1000 genomes]
rs1024568	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1024569	0.91[ASN][1000 genomes]
rs1024570	0.90[ASN][1000 genomes]
rs1024572	0.91[ASN][1000 genomes]
rs10260414	0.91[ASN][1000 genomes]
rs1029631	0.91[ASN][1000 genomes]
rs10500007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054043	0.91[ASN][1000 genomes]
rs10953712	0.90[ASN][1000 genomes]
rs10953713	0.91[ASN][1000 genomes]
rs11514940	0.91[ASN][1000 genomes]
rs11764489	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11769604	0.90[ASN][1000 genomes]
rs12154294	0.91[ASN][1000 genomes]
rs12531101	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12531636	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12539263	0.91[ASN][1000 genomes]
rs1468457	0.91[ASN][1000 genomes]
rs1468458	0.91[ASN][1000 genomes]
rs17159684	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17159686	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1963308	0.91[ASN][1000 genomes]
rs2190587	0.91[ASN][1000 genomes]
rs2396541	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2396542	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3095035	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34633971	0.91[ASN][1000 genomes]
rs36095669	0.91[ASN][1000 genomes]
rs3807206	0.91[ASN][1000 genomes]
rs3807210	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3807213	0.91[ASN][1000 genomes]
rs4275157	0.97[ASN][1000 genomes]
rs4727774	0.91[ASN][1000 genomes]
rs4730548	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730549	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55954386	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56020731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6944364	0.97[ASN][1000 genomes]
rs6945176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6963343	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6967593	0.99[ASN][1000 genomes]
rs6967894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6968084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6973615	0.91[ASN][1000 genomes]
rs73201469	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7455170	0.91[ASN][1000 genomes]
rs7777925	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7817	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	nsv831097	chr7:112000837-112113173	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1801262	chr7:112071795-112104179	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 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	chr7:112089200-112092600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr7:112089600-112092400	Active TSS	Fetal Intestine Small	intestine
3	chr7:112089600-112092600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr7:112089600-112092800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr7:112089600-112092800	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr7:112089600-112092800	Active TSS	Fetal Kidney	kidney
7	chr7:112089600-112093000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr7:112089600-112093000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:112089600-112093400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:112089600-112094000	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr7:112089600-112094200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr7:112089600-112094200	Active TSS	Psoas Muscle	Psoas
13	chr7:112089800-112092600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:112089800-112092600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:112089800-112092600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:112089800-112092600	Active TSS	Brain Cingulate Gyrus	brain
17	chr7:112089800-112092600	Active TSS	Esophagus	oesophagus
18	chr7:112089800-112092600	Active TSS	Lung	lung
19	chr7:112089800-112092800	Active TSS	Ovary	ovary
20	chr7:112089800-112092800	Active TSS	Pancreas	Pancrea
21	chr7:112089800-112093000	Active TSS	H1 Cell Line	embryonic stem cell
22	chr7:112089800-112093000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr7:112089800-112093000	Active TSS	Aorta	Aorta
24	chr7:112089800-112093000	Active TSS	Colon Smooth Muscle	Colon
25	chr7:112089800-112093000	Active TSS	Left Ventricle	heart
26	chr7:112089800-112093200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr7:112089800-112093400	Active TSS	A549	lung
28	chr7:112089800-112093600	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr7:112089800-112093600	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr7:112089800-112094400	Active TSS	Right Ventricle	heart
31	chr7:112089800-112094800	Active TSS	GM12878-XiMat	blood
32	chr7:112090000-112092400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr7:112090000-112092400	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr7:112090000-112092400	Active TSS	Fetal Intestine Large	intestine
35	chr7:112090000-112092400	Active TSS	Hela-S3	cervix
36	chr7:112090000-112092600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr7:112090000-112092600	Active TSS	Colonic Mucosa	Colon
38	chr7:112090000-112092600	Active TSS	Gastric	stomach
39	chr7:112090000-112092600	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr7:112090000-112092600	Active TSS	NHDF-Ad	bronchial
41	chr7:112090000-112092800	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr7:112090000-112092800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr7:112090000-112092800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr7:112090000-112092800	Active TSS	NHLF	lung
45	chr7:112090000-112094600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr7:112090200-112092400	Active TSS	Muscle Satellite Cultured Cells	--
47	chr7:112090200-112092400	Active TSS	NH-A	brain
48	chr7:112090200-112092600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr7:112090200-112092800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr7:112090200-112092800	Active TSS	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links