Variant report

Variant	rs62325241
Chromosome Location	chr4:99989284-99989285
allele	A/C
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	MAFK	chr4:99988712-99989590	HepG2	liver:	n/a	chr4:99988865-99988876 chr4:99989065-99989074 chr4:99988866-99988877 chr4:99988865-99988876 chr4:99988865-99988881
2	POLR2A	chr4:99989094-99989347	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:99989253-99989405	MCF-7	breast:	n/a	n/a
4	POLR2A	chr4:99987466-99989444	HepG2	liver:	n/a	n/a
5	POLR2A	chr4:99988457-99989373	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr4:99989139-99989546	PFSK-1	brain:	n/a	n/a
7	FOXA1	chr4:99988641-99989295	HepG2	liver:	n/a	n/a
8	POLR2A	chr4:99989093-99989409	HepG2	liver:	n/a	n/a
9	POLR2A	chr4:99988944-99989356	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr4:99987204-99993723	K562	blood:	n/a	n/a
11	POLR2A	chr4:99989231-99989465	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr4:99988814-99989448	HepG2	liver:	n/a	n/a
13	FOXA1	chr4:99988666-99989334	HepG2	liver:	n/a	n/a
14	POLR2A	chr4:99987215-99989453	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr4:99989139-99989295	K562	blood:	n/a	n/a
16	BCL3	chr4:99988859-99989461	K562	blood:	n/a	n/a
17	POLR2A	chr4:99989225-99989394	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr4:99987378-99990187	HepG2	liver:	n/a	n/a
19	POLR2A	chr4:99989068-99989388	U87	brain:	n/a	n/a
20	POLR2A	chr4:99988847-99989431	K562	blood:	n/a	n/a
21	POLR2A	chr4:99989281-99989389	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr4:99987770-99989410	HepG2	liver:	n/a	n/a
23	ZMIZ1	chr4:99989248-99989300	K562	blood:	n/a	n/a
24	MAFK	chr4:99988784-99989512	HepG2	liver:	n/a	chr4:99988865-99988876 chr4:99989065-99989074 chr4:99988866-99988877 chr4:99988865-99988876 chr4:99988865-99988881

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99987489..99989654-chr4:100009071..100011507,2	MCF-7	breast:
2	chr4:99849436..99851753-chr4:99986729..99991688,5	K562	blood:

Variant related genes	Relation type
ENSG00000272777	TF binding region
ENSG00000151247	Chromatin interaction
ENSG00000246090	Chromatin interaction
ENSG00000238449	Chromatin interaction
ENSG00000263923	Chromatin interaction
ENSG00000197894	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10002449	0.81[EUR][1000 genomes]
rs10084896	0.81[EUR][1000 genomes]
rs17028370	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17028473	0.90[AFR][1000 genomes]
rs17028758	0.85[AMR][1000 genomes]
rs2051429	0.85[AMR][1000 genomes]
rs28720156	0.83[AMR][1000 genomes]
rs28730581	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730584	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730596	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730601	0.96[EUR][1000 genomes]
rs28730610	0.84[AFR][1000 genomes]
rs28730611	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730617	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730625	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730641	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730643	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730644	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730645	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730646	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730649	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28894370	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28894371	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs29001228	0.83[AMR][1000 genomes]
rs29001338	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs29001342	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs29001346	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs29001348	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs29001631	0.85[AFR][1000 genomes]
rs4499706	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5003497	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55831712	0.81[EUR][1000 genomes]
rs61431883	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323213	0.81[EUR][1000 genomes]
rs62323214	0.81[EUR][1000 genomes]
rs62323216	0.81[EUR][1000 genomes]
rs62323217	0.81[EUR][1000 genomes]
rs62323230	0.81[EUR][1000 genomes]
rs62323231	0.81[EUR][1000 genomes]
rs62323233	0.81[EUR][1000 genomes]
rs62323234	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323235	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323236	0.81[EUR][1000 genomes]
rs62323237	0.81[EUR][1000 genomes]
rs62323238	0.81[EUR][1000 genomes]
rs62323240	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323241	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323242	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323244	0.81[EUR][1000 genomes]
rs62323245	0.83[AMR][1000 genomes]
rs62323246	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323247	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323248	0.81[EUR][1000 genomes]
rs62323249	0.81[EUR][1000 genomes]
rs62323250	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323251	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323252	0.81[EUR][1000 genomes]
rs62323253	0.81[EUR][1000 genomes]
rs62323254	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323255	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323256	0.81[EUR][1000 genomes]
rs62323257	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323258	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323259	0.81[EUR][1000 genomes]
rs62325160	0.81[EUR][1000 genomes]
rs62325161	0.81[EUR][1000 genomes]
rs62325182	0.81[EUR][1000 genomes]
rs62325183	0.81[EUR][1000 genomes]
rs62325184	0.81[EUR][1000 genomes]
rs62325185	0.81[EUR][1000 genomes]
rs62325186	0.81[EUR][1000 genomes]
rs62325187	0.81[EUR][1000 genomes]
rs62325188	0.81[EUR][1000 genomes]
rs62325189	0.81[EUR][1000 genomes]
rs62325192	0.81[EUR][1000 genomes]
rs62325193	0.81[EUR][1000 genomes]
rs62325194	0.81[EUR][1000 genomes]
rs62325195	0.81[EUR][1000 genomes]
rs62325196	0.81[EUR][1000 genomes]
rs62325197	0.81[EUR][1000 genomes]
rs62325198	0.81[EUR][1000 genomes]
rs62325199	0.81[EUR][1000 genomes]
rs62325200	0.81[EUR][1000 genomes]
rs62325201	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325202	0.81[EUR][1000 genomes]
rs62325203	0.81[EUR][1000 genomes]
rs62325204	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325205	0.81[EUR][1000 genomes]
rs62325206	0.81[EUR][1000 genomes]
rs62325208	0.81[EUR][1000 genomes]
rs62325209	0.81[EUR][1000 genomes]
rs62325210	0.81[EUR][1000 genomes]
rs62325211	0.81[EUR][1000 genomes]
rs62325212	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325213	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325236	0.81[EUR][1000 genomes]
rs62325237	0.81[EUR][1000 genomes]
rs62325238	0.81[EUR][1000 genomes]
rs62325239	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325240	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325242	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325245	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6532781	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6532792	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6819694	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6819724	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6822742	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6823388	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6827292	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72897156	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72897165	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72897167	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7664906	0.85[AFR][1000 genomes]
rs7667261	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7679102	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7681427	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7687322	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7688859	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7699232	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9995869	0.81[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	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62325241	ADH5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99954000-99999200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:99956200-99995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:99959800-100000200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:99971800-99991600	Weak transcription	Brain Anterior Caudate	brain
5	chr4:99971800-99997600	Weak transcription	Spleen	Spleen
6	chr4:99974000-99993000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:99976000-99989800	Weak transcription	Fetal Brain Female	brain
8	chr4:99976400-99992800	Weak transcription	Aorta	Aorta
9	chr4:99977200-99994400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:99977400-99991600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:99977400-99992800	Weak transcription	Brain Substantia Nigra	brain
12	chr4:99977400-99994800	Weak transcription	Right Atrium	heart
13	chr4:99977400-99996600	Weak transcription	Brain Angular Gyrus	brain
14	chr4:99977400-99996800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr4:99977400-99997000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:99977600-100008400	Weak transcription	Stomach Mucosa	stomach
17	chr4:99977800-100009000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:99978000-100007800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:99979800-99992800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:99979800-99994800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:99980000-99992600	Weak transcription	Colonic Mucosa	Colon
22	chr4:99980000-99993000	Weak transcription	Ovary	ovary
23	chr4:99980000-99995000	Weak transcription	Small Intestine	intestine
24	chr4:99980000-99997000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr4:99980200-99993000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:99980400-99991400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:99981000-99992400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr4:99981200-99992400	Weak transcription	Brain Germinal Matrix	brain
29	chr4:99981200-99997000	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:99982000-99990000	Weak transcription	Placenta	Placenta
31	chr4:99982400-99995000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr4:99982400-99997000	Weak transcription	Hela-S3	cervix
33	chr4:99982400-100000400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:99982600-99991600	Weak transcription	NHLF	lung
35	chr4:99982600-99992000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:99982600-99992400	Weak transcription	NHEK	skin
37	chr4:99982600-99992600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr4:99982600-99996000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:99982800-99989800	Weak transcription	Fetal Stomach	stomach
40	chr4:99982800-99993000	Weak transcription	Left Ventricle	heart
41	chr4:99982800-99996000	Weak transcription	Gastric	stomach
42	chr4:99982800-100000200	Weak transcription	Psoas Muscle	Psoas
43	chr4:99983000-99991600	Weak transcription	Brain Hippocampus Middle	brain
44	chr4:99983000-100004600	Weak transcription	Pancreas	Pancrea
45	chr4:99983200-99992400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr4:99983200-99992800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr4:99983200-100000200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:99983200-100008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr4:99983400-99990600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:99983400-99991000	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links