Variant report

Variant	rs6656337
Chromosome Location	chr1:45245591-45245592
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:62)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:62 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45243922-45247518	U87	brain:	n/a	n/a
2	POLR2A	chr1:45243842-45247542	A549	lung:	n/a	n/a
3	POLR2A	chr1:45240631-45247540	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:45240526-45248028	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:45245136-45247601	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr1:45240483-45248016	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:45240295-45248263	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:45242580-45247462	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr1:45245435-45247654	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:45245486-45245937	GM18505	blood:	n/a	n/a
11	POLR2A	chr1:45240547-45249219	HepG2	liver:	n/a	n/a
12	PML	chr1:45245192-45245653	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:45239529-45250168	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr1:45245346-45247310	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:45245270-45247449	K562	blood:	n/a	n/a
16	HEY1	chr1:45245231-45247342	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:45245558-45247137	K562	blood:	n/a	n/a
18	POLR2A	chr1:45245586-45246157	HCT-116	colon:	n/a	n/a
19	POLR2A	chr1:45245246-45247630	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr1:45245356-45245984	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr1:45242766-45248217	GM12891	blood:	n/a	n/a
22	POLR2A	chr1:45242928-45247383	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr1:45245346-45248048	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr1:45245249-45247425	GM12891	blood:	n/a	n/a
25	POLR2A	chr1:45245234-45247606	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr1:45240546-45248272	GM12892	blood:	n/a	n/a
27	POLR2A	chr1:45242629-45247224	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr1:45243708-45245616	K562	blood:	n/a	n/a
29	POLR2A	chr1:45245542-45245731	MCF-7	breast:	n/a	n/a
30	POLR2A	chr1:45245563-45247412	Hela-S3	cervix:	n/a	n/a
31	HEY1	chr1:45245582-45247381	HepG2	liver:	n/a	n/a
32	POLR2A	chr1:45245288-45247341	K562	blood:	n/a	n/a
33	POLR2A	chr1:45245243-45246088	HL-60	blood:	n/a	n/a
34	POLR2A	chr1:45240508-45247317	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:45240713-45247745	PFSK-1	brain:	n/a	n/a
36	POLR2A	chr1:45243853-45247621	U87	brain:	n/a	n/a
37	POLR2A	chr1:45245340-45247541	HepG2	liver:	n/a	n/a
38	POLR2A	chr1:45240271-45247480	K562	blood:	n/a	n/a
39	POLR2A	chr1:45245085-45249976	PANC-1	pancreas:	n/a	n/a
40	POLR2A	chr1:45245220-45246102	HL-60	blood:	n/a	n/a
41	POLR2A	chr1:45239953-45247379	K562	blood:	n/a	n/a
42	POLR2A	chr1:45240502-45248124	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:45245541-45247575	MCF-7	breast:	n/a	n/a
44	POLR2A	chr1:45240539-45248722	PFSK-1	brain:	n/a	n/a
45	POLR2A	chr1:45240524-45248015	GM12891	blood:	n/a	n/a
46	POLR2A	chr1:45245305-45248679	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr1:45245333-45247464	K562	blood:	n/a	n/a
48	POLR2A	chr1:45245470-45247287	HEK293	kidney:	n/a	n/a
49	POLR2A	chr1:45245308-45245622	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr1:45245300-45248111	GM12891	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
2	chr1:45245131..45247941-chr1:45805894..45808200,2	K562	blood:
3	chr1:45239959..45246724-chr1:45282430..45287057,13	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225721	TF binding region
ENSG00000173846	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000222009	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10127448	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10465818	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211030	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211031	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211034	0.87[ASN][1000 genomes]
rs11584031	0.83[ASN][1000 genomes]
rs11801067	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11808189	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11808852	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12094028	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12117881	0.81[ASN][1000 genomes]
rs12136048	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12136099	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12742914	0.82[ASN][1000 genomes]
rs16832228	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4542248	0.87[EUR][1000 genomes]
rs6429548	0.88[EUR][1000 genomes]
rs6658470	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6666987	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6671255	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6678729	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6685176	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6688710	0.92[ASN][1000 genomes]
rs6698847	0.81[ASN][1000 genomes]
rs7512710	0.90[ASN][1000 genomes]
rs7518836	0.85[ASN][1000 genomes]
rs7524446	0.81[EUR][1000 genomes]
rs7536146	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7550170	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7555065	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9988580	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases
8	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
10	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
11	nsv947252	chr1:45242176-45258816	Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
12	nsv945912	chr1:45243841-45248516	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	16 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	chr1:45242400-45246400	Strong transcription	Aorta	Aorta
2	chr1:45242600-45247600	Strong transcription	Brain Hippocampus Middle	brain
3	chr1:45242800-45247400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:45242800-45247800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:45243000-45245600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:45243000-45246600	Strong transcription	Brain Anterior Caudate	brain
7	chr1:45243000-45247200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:45243200-45246200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:45243200-45246400	Strong transcription	HSMMtube	muscle
10	chr1:45243200-45247000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:45243200-45247400	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:45243400-45246800	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:45243400-45247200	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr1:45243400-45247400	Strong transcription	Liver	Liver
15	chr1:45243400-45248200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr1:45243400-45249000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:45243600-45245600	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr1:45243600-45245800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:45243600-45246600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:45243600-45246800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:45243600-45247200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:45243600-45247200	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:45243600-45247200	Strong transcription	Lung	lung
24	chr1:45243600-45247200	Strong transcription	Spleen	Spleen
25	chr1:45243600-45247400	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr1:45243600-45247400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:45243600-45247400	Strong transcription	Esophagus	oesophagus
28	chr1:45243600-45248000	Strong transcription	Fetal Brain Female	brain
29	chr1:45243600-45248200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:45243600-45249000	Strong transcription	Primary B cells from cord blood	blood
31	chr1:45243600-45249400	Weak transcription	Right Atrium	heart
32	chr1:45243800-45247200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:45243800-45248000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:45244000-45247000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr1:45244000-45247200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:45244000-45247200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:45244000-45247200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:45244000-45247200	Strong transcription	Fetal Intestine Large	intestine
39	chr1:45244000-45247200	Strong transcription	Left Ventricle	heart
40	chr1:45244000-45247400	Strong transcription	Colonic Mucosa	Colon
41	chr1:45244000-45249000	Weak transcription	Fetal Lung	lung
42	chr1:45244000-45249800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:45244000-45249800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr1:45244200-45245600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:45244200-45246000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:45244200-45246600	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:45244200-45247000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:45244200-45247200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:45244200-45247200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:45244200-45247200	Strong transcription	Adipose Nuclei	Adipose

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