Variant report

Variant	rs4522000
Chromosome Location	chr1:151256088-151256089
allele	C/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	POLR2A	chr1:151253351-151256536	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr1:151253485-151256229	HepG2	liver:	n/a	chr1:151255644-151255654 chr1:151256051-151256061 chr1:151255641-151255651
3	POLR2A	chr1:151253247-151256985	GM12878	blood:	n/a	n/a
4	ELF1	chr1:151253418-151256101	GM12878	blood:	n/a	chr1:151255831-151255844 chr1:151255378-151255390
5	POLR2A	chr1:151253560-151256282	K562	blood:	n/a	n/a
6	ELF1	chr1:151255509-151256092	GM12878	blood:	n/a	chr1:151255831-151255844
7	MAX	chr1:151253298-151256115	MCF-7	breast:	n/a	chr1:151255644-151255654 chr1:151256051-151256061 chr1:151255641-151255651
8	POLR2A	chr1:151253493-151256729	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:151253356-151256415	GM12892	blood:	n/a	n/a
10	STAT1	chr1:151256065-151256171	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:151253538-151256270	GM12891	blood:	n/a	n/a
12	POLR2A	chr1:151253502-151256147	GM12891	blood:	n/a	n/a
13	POLR2A	chr1:151253457-151256217	HL-60	blood:	n/a	n/a
14	NR2F2	chr1:151255287-151256235	K562	blood:	n/a	chr1:151255999-151256014
15	POLR2A	chr1:151253470-151256391	GM12891	blood:	n/a	n/a
16	RUNX3	chr1:151255526-151256239	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:151253411-151256493	K562	blood:	n/a	n/a
18	POLR2A	chr1:151253465-151256184	K562	blood:	n/a	n/a
19	HCFC1	chr1:151253385-151256875	Hela-S3	cervix:	n/a	n/a
20	NR2F2	chr1:151253300-151256257	MCF-7	breast:	n/a	chr1:151255999-151256014
21	MAZ	chr1:151253475-151256397	IMR90	lung:	n/a	chr1:151255644-151255654 chr1:151256051-151256061 chr1:151255641-151255651
22	SIN3AK20	chr1:151253204-151256272	MCF-7	breast:	n/a	n/a
23	POLR2A	chr1:151253398-151256170	GM12892	blood:	n/a	n/a
24	POLR2A	chr1:151253509-151256101	GM19193	blood:	n/a	n/a
25	MTA3	chr1:151253293-151256545	GM12878	blood:	n/a	n/a
26	EGR1	chr1:151255913-151256140	GM12878	blood:	n/a	chr1:151256049-151256063 chr1:151256051-151256061 chr1:151256047-151256062 chr1:151256048-151256061 chr1:151256048-151256061
27	EGR1	chr1:151255711-151256213	K562	blood:	n/a	chr1:151255874-151255887 chr1:151256049-151256063 chr1:151256051-151256061 chr1:151256047-151256062 chr1:151255879-151255889 chr1:151256048-151256061 chr1:151256048-151256061
28	MAX	chr1:151253162-151256180	MCF-7	breast:	n/a	chr1:151255644-151255654 chr1:151256051-151256061 chr1:151255641-151255651
29	HEY1	chr1:151253453-151256128	HepG2	liver:	n/a	chr1:151255520-151255535 chr1:151255373-151255388
30	POLR2A	chr1:151253461-151256114	HepG2	liver:	n/a	n/a
31	ELF1	chr1:151253215-151256110	MCF-7	breast:	n/a	chr1:151255831-151255844 chr1:151255378-151255390
32	POLR2A	chr1:151253537-151256168	K562	blood:	n/a	n/a
33	EGR1	chr1:151255786-151256202	K562	blood:	n/a	chr1:151255874-151255887 chr1:151256049-151256063 chr1:151256051-151256061 chr1:151256047-151256062 chr1:151255879-151255889 chr1:151256048-151256061 chr1:151256048-151256061
34	POLR2A	chr1:151253282-151256108	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:151253369-151257288	GM12878	blood:	n/a	n/a
36	CTCF	chr1:151255960-151256110	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151252318..151256662-chr1:151278805..151282568,3	MCF-7	breast:
2	chr1:151236628..151240261-chr1:151252418..151256646,5	K562	blood:
3	chr1:151254308..151256785-chr1:151512305..151514288,3	MCF-7	breast:
4	chr1:151253853..151259248-chr1:151295350..151301325,11	K562	blood:
5	chr1:151254636..151256899-chr1:151735426..151737662,3	MCF-7	breast:
6	chr1:151165541..151174157-chr1:151252015..151257857,16	MCF-7	breast:
7	chr1:151253871..151256135-chr1:151314130..151317235,4	K562	blood:
8	chr1:151255364..151257714-chr1:151311945..151313643,2	MCF-7	breast:
9	chr1:151254429..151257729-chr1:151370560..151375073,7	MCF-7	breast:
10	chr1:151161155..151162888-chr1:151254618..151258389,3	MCF-7	breast:
11	chr1:151252184..151258894-chr1:151295105..151301119,15	MCF-7	breast:
12	chr1:151254330..151257054-chr1:151298258..151300253,2	K562	blood:
13	chr1:151168724..151174586-chr1:151252405..151256834,10	MCF-7	breast:
14	chr1:151254480..151256114-chr6:26019497..26022258,2	MCF-7	breast:
15	1:151254384-151268403..1:151402394-151411623	GM12878	blood:
16	chr1:151253109..151257431-chr1:151311446..151315369,6	MCF-7	breast:
17	chr1:151161802..151163461-chr1:151255250..151256972,2	MCF-7	breast:
18	chr1:151162643..151164803-chr1:151253771..151256720,2	K562	blood:
19	chr1:151252229..151256416-chr1:151370480..151373573,6	MCF-7	breast:
20	chr1:151241727..151244431-chr1:151255120..151256643,2	MCF-7	breast:
21	chr1:151254955..151256703-chr1:151342401..151344632,2	MCF-7	breast:
22	chr1:151225526..151228725-chr1:151252382..151257550,9	K562	blood:
23	chr1:151042356..151044958-chr1:151252271..151256325,4	K562	blood:
24	chr1:151253682..151256795-chr1:151298712..151301104,5	MCF-7	breast:
25	chr1:151253871..151258133-chr1:151311236..151320814,17	K562	blood:
26	1:151171193-151178589..1:151254384-151268403	Hela-S3	cervix:
27	chr1:151252692..151257354-chr1:151370358..151373702,7	K562	blood:
28	chr1:151253402..151256437-chr1:151318501..151320102,3	MCF-7	breast:
29	chr1:151254608..151256601-chr11:68517893..68520689,2	MCF-7	breast:
30	chr1:151222463..151229121-chr1:151253476..151256667,10	MCF-7	breast:
31	chr1:151225998..151229280-chr1:151252382..151256725,6	K562	blood:
32	chr1:151224415..151228832-chr1:151251866..151257138,17	MCF-7	breast:
33	chr1:151252566..151256216-chr1:151370228..151373702,9	K562	blood:

Variant related genes	Relation type
ZNF687	TF binding region
ENSG00000232671	TF binding region
ENSG00000197622	Chromatin interaction
ENSG00000159377	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000143450	Chromatin interaction
ENSG00000143416	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000238711	Chromatin interaction
ENSG00000224645	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000237976	Chromatin interaction
ENSG00000273481	Chromatin interaction
ENSG00000132749	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000143436	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000143390	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000196176	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1056847	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10788803	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10888408	0.88[ASN][1000 genomes]
rs10888409	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10888410	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888411	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11204791	0.88[ASN][1000 genomes]
rs11204795	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12048670	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12407426	0.80[ASN][1000 genomes]
rs16827941	0.80[ASN][1000 genomes]
rs2275900	0.88[ASN][1000 genomes]
rs41302131	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4246525	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970948	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4971023	0.80[ASN][1000 genomes]
rs4971025	0.88[ASN][1000 genomes]
rs4971026	0.88[ASN][1000 genomes]
rs4971027	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4971030	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4971031	0.91[EUR][1000 genomes]
rs4971032	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4971033	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5022636	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6587559	0.80[ASN][1000 genomes]
rs6587562	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6681071	0.86[ASN][1000 genomes]
rs6681163	0.86[ASN][1000 genomes]
rs6686402	0.80[ASN][1000 genomes]
rs6701325	0.80[ASN][1000 genomes]
rs7518924	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7527032	0.80[ASN][1000 genomes]
rs7532935	0.80[ASN][1000 genomes]
rs7544947	0.80[ASN][1000 genomes]
rs7545392	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7552906	0.86[EUR][1000 genomes]
rs943637	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
2	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
3	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
4	esv2754960	chr1:151240542-151331304	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	esv34461	chr1:151240542-151411635	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	esv2753774	chr1:151240542-151411635	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151253400-151256200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:151253400-151256200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr1:151253400-151256200	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr1:151253400-151256200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr1:151253400-151256200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:151253400-151256200	Active TSS	HSMMtube	muscle
7	chr1:151253400-151256400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:151253400-151256600	Active TSS	A549	lung
9	chr1:151253400-151256800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr1:151253600-151256200	Active TSS	Brain Anterior Caudate	brain
11	chr1:151253800-151256200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:151253800-151256200	Active TSS	Fetal Intestine Large	intestine
13	chr1:151253800-151256200	Active TSS	Fetal Intestine Small	intestine
14	chr1:151254000-151256200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:151254000-151256200	Active TSS	Ovary	ovary
16	chr1:151254000-151256200	Active TSS	NHDF-Ad	bronchial
17	chr1:151255000-151256600	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr1:151255000-151256800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr1:151255200-151256400	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr1:151255200-151256400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:151255200-151256400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr1:151255200-151256400	Flanking Active TSS	Brain Germinal Matrix	brain
23	chr1:151255200-151256600	Flanking Active TSS	Fetal Brain Female	brain
24	chr1:151255200-151256800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr1:151255200-151257000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:151255400-151256200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr1:151255400-151256200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr1:151255400-151256200	Flanking Active TSS	Fetal Muscle Trunk	muscle
29	chr1:151255400-151256200	Flanking Active TSS	Fetal Thymus	thymus
30	chr1:151255400-151256400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:151255400-151256400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr1:151255400-151256400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr1:151255400-151256400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr1:151255400-151256400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:151255400-151256400	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr1:151255400-151256400	Flanking Active TSS	HMEC	breast
37	chr1:151255400-151256600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:151255400-151256600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr1:151255400-151256600	Flanking Active TSS	NHEK	skin
40	chr1:151255400-151256800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr1:151255400-151256800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr1:151255400-151256800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:151255400-151256800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:151255400-151256800	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr1:151255400-151256800	Flanking Active TSS	Dnd41	blood
46	chr1:151255400-151256800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr1:151255400-151257000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:151255600-151256200	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr1:151255600-151256200	Flanking Active TSS	Esophagus	oesophagus
50	chr1:151255600-151256200	Flanking Active TSS	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links