Variant report

Variant	rs9645347
Chromosome Location	chr1:45286972-45286973
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:35)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:45286792-45287019	K562	blood:	n/a	n/a
2	POLR2A	chr1:45284719-45287102	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:45283633-45286977	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr1:45283034-45287112	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:45284835-45290143	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:45284731-45286977	A549	lung:	n/a	n/a
7	CTCF	chr1:45286880-45287030	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:45286878-45287004	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:35 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45283976..45287622-chr1:45450715..45458034,11	K562	blood:
2	chr1:45286163..45288443-chr1:45670899..45672707,2	MCF-7	breast:
3	chr1:45246681..45259677-chr1:45281336..45290057,25	MCF-7	breast:
4	chr1:45183794..45190315-chr1:45281186..45287888,32	MCF-7	breast:
5	chr1:45190324..45200952-chr1:45272085..45288310,59	MCF-7	breast:
6	chr1:45283441..45287322-chr1:45806283..45809735,5	K562	blood:
7	chr1:45285223..45287431-chr1:45796850..45798440,2	K562	blood:
8	chr1:45283510..45287262-chr1:45964108..45968951,6	K562	blood:
9	chr1:45282320..45290015-chr1:45470338..45482903,45	K562	blood:
10	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
11	chr1:45284581..45287931-chr1:45452240..45453906,3	MCF-7	breast:
12	chr1:45285229..45287089-chr6:27114044..27115852,2	K562	blood:
13	chr1:45284131..45287086-chr1:46150918..46155233,4	K562	blood:
14	chr1:45193443..45200768-chr1:45280884..45289784,25	MCF-7	breast:
15	chr1:45282917..45288387-chr1:45449365..45456835,12	K562	blood:
16	chr1:45283391..45288738-chr1:46048072..46051277,6	K562	blood:
17	chr1:45138628..45142139-chr1:45284311..45287293,3	K562	blood:
18	chr1:45282552..45287322-chr1:45800975..45809178,15	K562	blood:
19	chr1:45138846..45140419-chr1:45285413..45286988,2	K562	blood:
20	chr1:45285788..45287564-chr1:45957142..45958713,2	K562	blood:
21	chr1:45284268..45287037-chr1:45476110..45479807,4	MCF-7	breast:
22	chr1:45096122..45099489-chr1:45284877..45287072,3	K562	blood:
23	chr1:45284891..45287044-chr6:43595732..43598640,2	K562	blood:
24	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
25	chr1:45286428..45288108-chr1:45735676..45738640,2	K562	blood:
26	chr1:45283389..45288095-chr1:45474959..45480313,6	MCF-7	breast:
27	chr1:45284392..45287262-chr1:45964108..45967526,3	K562	blood:
28	chr1:45281186..45291350-chr1:45463934..45483092,44	K562	blood:
29	chr1:45239959..45246724-chr1:45282430..45287057,13	MCF-7	breast:
30	chr1:45179633..45191596-chr1:45283435..45288613,20	MCF-7	breast:
31	chr1:45282609..45288514-chr1:45767803..45773154,13	K562	blood:
32	chr1:45284090..45287076-chr1:45986937..45989870,4	K562	blood:
33	chr1:45285566..45287253-chr15:75197624..75199346,2	MCF-7	breast:
34	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:
35	chr1:45239429..45243402-chr1:45282541..45287001,15	MCF-7	breast:

No data

Variant related genes	Relation type
RNU5E-6P	TF binding region
ENSG00000132780	Chromatin interaction
ENSG00000234093	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000172432	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000142959	Chromatin interaction
ENSG00000126106	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000187147	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000070785	Chromatin interaction
ENSG00000124688	Chromatin interaction
ENSG00000232369	Chromatin interaction
ENSG00000268949	Chromatin interaction
ENSG00000197903	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10158188	0.88[EUR][1000 genomes]
rs10465818	0.81[ASN][1000 genomes]
rs11211031	0.80[ASN][1000 genomes]
rs11211034	0.84[ASN][1000 genomes]
rs11211037	0.85[EUR][1000 genomes]
rs11211044	0.93[EUR][1000 genomes]
rs11211046	0.93[EUR][1000 genomes]
rs11211047	0.93[EUR][1000 genomes]
rs11584031	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12036829	0.89[ASN][1000 genomes]
rs12094007	0.91[EUR][1000 genomes]
rs12117881	0.84[ASN][1000 genomes]
rs12118515	0.92[EUR][1000 genomes]
rs12120470	0.92[EUR][1000 genomes]
rs12144803	0.92[EUR][1000 genomes]
rs12408818	0.93[EUR][1000 genomes]
rs12568071	0.92[EUR][1000 genomes]
rs12568279	0.92[EUR][1000 genomes]
rs2273940	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263962	0.89[EUR][1000 genomes]
rs263965	0.90[EUR][1000 genomes]
rs263975	0.89[EUR][1000 genomes]
rs263977	0.89[EUR][1000 genomes]
rs263986	0.88[ASN][1000 genomes]
rs3795720	0.92[EUR][1000 genomes]
rs621630	0.88[ASN][1000 genomes]
rs6688465	0.92[EUR][1000 genomes]
rs6696675	0.93[EUR][1000 genomes]
rs6698951	0.93[EUR][1000 genomes]
rs746320	0.93[EUR][1000 genomes]
rs7514741	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525308	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526786	0.81[EUR][1000 genomes]
rs7545808	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554177	0.91[EUR][1000 genomes]
rs932691	0.93[EUR][1000 genomes]
rs9988451	0.89[EUR][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	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
8	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
9	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
10	nsv546146	chr1:45258141-45318752	Genic enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	109 gene(s)	inside rSNPs	diseases
11	nsv870773	chr1:45259295-45287306	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS 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	108 gene(s)	inside rSNPs	diseases
12	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45284600-45287000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:45285600-45292400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:45285800-45287000	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr1:45286200-45287000	Weak transcription	Brain Germinal Matrix	brain
5	chr1:45286200-45287000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:45286200-45287200	Enhancers	Spleen	Spleen
7	chr1:45286200-45288000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:45286200-45288200	Weak transcription	Ovary	ovary
9	chr1:45286200-45301800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:45286400-45287000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr1:45286400-45287000	Enhancers	Esophagus	oesophagus
12	chr1:45286400-45287000	Genic enhancers	Fetal Stomach	stomach
13	chr1:45286400-45287200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr1:45286400-45287200	Enhancers	Brain Substantia Nigra	brain
15	chr1:45286400-45287200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:45286400-45287200	Enhancers	Fetal Lung	lung
17	chr1:45286400-45287200	Enhancers	Fetal Muscle Leg	muscle
18	chr1:45286400-45287200	Flanking Active TSS	HepG2	liver
19	chr1:45286400-45287400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr1:45286400-45287400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr1:45286400-45287400	Enhancers	Stomach Mucosa	stomach
22	chr1:45286400-45288200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:45286400-45288600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:45286400-45292000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:45286400-45308400	Weak transcription	Aorta	Aorta
26	chr1:45286600-45287000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:45286600-45287000	Enhancers	Primary T cells from cord blood	blood
28	chr1:45286600-45287000	Enhancers	Primary hematopoietic stem cells	blood
29	chr1:45286600-45287000	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr1:45286600-45287000	Enhancers	Fetal Thymus	thymus
31	chr1:45286600-45287000	Enhancers	Left Ventricle	heart
32	chr1:45286600-45287000	Enhancers	Thymus	Thymus
33	chr1:45286600-45287200	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr1:45286600-45287200	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr1:45286600-45287200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:45286600-45287200	Enhancers	Colonic Mucosa	Colon
37	chr1:45286600-45287200	Enhancers	Fetal Muscle Trunk	muscle
38	chr1:45286600-45287200	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr1:45286600-45287200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr1:45286600-45287400	Enhancers	Primary T cells fromperipheralblood	blood
41	chr1:45286600-45287400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:45286600-45287400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:45286600-45287400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:45286600-45287400	Enhancers	Lung	lung
45	chr1:45286600-45287400	Enhancers	Pancreas	Pancrea
46	chr1:45286600-45288000	Weak transcription	GM12878-XiMat	blood
47	chr1:45286600-45288600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:45286600-45288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:45286600-45289000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:45286600-45289000	Strong transcription	Fetal Brain Female	brain

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