Variant report

Variant	rs12404244
Chromosome Location	chr1:45276620-45276621
allele	A/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	chr1:45270630-45276680	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:45270697-45276683	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:45272295-45276658	GM12891	blood:	n/a	n/a
4	POLR2A	chr1:45272557-45276628	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr1:45272231-45276688	SK-N-SH	brain:	n/a	n/a
6	MAZ	chr1:45272345-45276629	IMR90	lung:	n/a	chr1:45273101-45273110 chr1:45274140-45274149 chr1:45272888-45272897 chr1:45272902-45272912 chr1:45273819-45273828 chr1:45273217-45273226 chr1:45272889-45272898 chr1:45273195-45273211 chr1:45274136-45274145 chr1:45275856-45275866
7	POLR2A	chr1:45272349-45276663	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:45271526-45276700	GM12892	blood:	n/a	n/a
9	POLR2A	chr1:45276243-45276639	GM12892	blood:	n/a	n/a
10	POLR2A	chr1:45270812-45279067	A549	lung:	n/a	n/a
11	POLR2A	chr1:45272451-45276703	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr1:45272178-45276714	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr1:45272346-45276630	IMR90	lung:	n/a	n/a
14	SPI1	chr1:45275760-45276738	GM12878	blood:	n/a	chr1:45275866-45275879

No.	Distal block	Cell Line	Cell type
1	chr1:45190324..45200952-chr1:45272085..45288310,59	MCF-7	breast:
2	chr1:45184399..45189674-chr1:45270870..45279135,15	MCF-7	breast:
3	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
4	chr1:45194189..45198394-chr1:45270401..45277394,13	MCF-7	breast:
5	chr1:45241279..45243837-chr1:45275916..45278923,3	MCF-7	breast:
6	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
7	chr1:45272934..45277358-chr1:45964626..45967668,4	K562	blood:
8	chr1:45239942..45244585-chr1:45273690..45277023,5	MCF-7	breast:
9	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:

Variant related genes	Relation type
BTBD19	TF binding region
TCTEX1D4	TF binding region
ENSG00000199377	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000234093	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000142959	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11211042	0.85[ASN][1000 genomes]
rs11211043	0.84[ASN][1000 genomes]
rs12095412	0.85[ASN][1000 genomes]
rs12404160	0.94[EUR][1000 genomes]
rs12405110	0.89[ASN][1000 genomes]
rs12407290	0.91[EUR][1000 genomes]
rs16832249	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16832251	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17883304	0.91[EUR][1000 genomes]
rs17885815	0.92[EUR][1000 genomes]
rs2295996	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3795718	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3923304	0.91[EUR][1000 genomes]
rs4073112	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269085	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4520451	0.94[EUR][1000 genomes]
rs4565758	0.91[EUR][1000 genomes]
rs59803789	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60189524	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60766209	0.89[ASN][1000 genomes]
rs6657078	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6678737	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72674049	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72674051	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45270000-45278200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:45271800-45277400	Weak transcription	Ovary	ovary
3	chr1:45272000-45278000	Enhancers	Primary hematopoietic stem cells	blood
4	chr1:45272400-45277600	Enhancers	Primary B cells from peripheral blood	blood
5	chr1:45272600-45276800	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr1:45272600-45277000	Enhancers	Lung	lung
7	chr1:45272800-45277600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:45272800-45278000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:45273000-45278000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:45273400-45278000	Enhancers	Brain Substantia Nigra	brain
11	chr1:45273600-45277600	Enhancers	Gastric	stomach
12	chr1:45274000-45278000	Enhancers	Thymus	Thymus
13	chr1:45274200-45279200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr1:45274400-45279000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:45274800-45277000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr1:45274800-45278000	Enhancers	Hela-S3	cervix
17	chr1:45274800-45278200	Weak transcription	Fetal Heart	heart
18	chr1:45274800-45278400	Weak transcription	Fetal Brain Female	brain
19	chr1:45274800-45278600	Enhancers	Brain Angular Gyrus	brain
20	chr1:45274800-45279000	Enhancers	Fetal Thymus	thymus
21	chr1:45275000-45277600	Enhancers	Right Ventricle	heart
22	chr1:45275000-45278200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:45275000-45278400	Weak transcription	Fetal Brain Male	brain
24	chr1:45275000-45278600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:45275000-45278600	Enhancers	Brain Anterior Caudate	brain
26	chr1:45275000-45278600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:45275000-45278800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:45275000-45279000	Genic enhancers	Placenta	Placenta
29	chr1:45275200-45278200	Enhancers	K562	blood
30	chr1:45275200-45278800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:45275200-45278800	Enhancers	Right Atrium	heart
32	chr1:45275200-45279000	Enhancers	Primary T cells fromperipheralblood	blood
33	chr1:45275200-45279400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr1:45275400-45278000	Enhancers	Fetal Muscle Leg	muscle
35	chr1:45275400-45278200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr1:45275400-45278800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:45275400-45278800	Enhancers	Placenta Amnion	Placenta Amnion
38	chr1:45275400-45279200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:45275400-45279200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr1:45275600-45277400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:45275600-45277400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:45275600-45278000	Genic enhancers	Fetal Muscle Trunk	muscle
43	chr1:45275600-45278600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:45275600-45278600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:45275600-45278600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:45275600-45278600	Weak transcription	Brain Germinal Matrix	brain
47	chr1:45275600-45278800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:45275800-45276800	Enhancers	Rectal Smooth Muscle	rectum
49	chr1:45275800-45277200	Enhancers	Primary B cells from cord blood	blood
50	chr1:45275800-45277400	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links