Variant report

Variant	rs3795718
Chromosome Location	chr1:45276427-45276428
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	RUNX3	chr1:45274662-45276517	GM12878	blood:	n/a	n/a
3	PAX5	chr1:45275047-45276443	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:45270697-45276683	GM12892	blood:	n/a	n/a
5	RELA	chr1:45274946-45276608	GM19193	blood:	n/a	n/a
6	POLR2A	chr1:45276100-45276516	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:45272295-45276658	GM12891	blood:	n/a	n/a
8	RELA	chr1:45274785-45276509	GM12891	blood:	n/a	n/a
9	NFIC	chr1:45274237-45276485	GM12878	blood:	n/a	n/a
10	FOXM1	chr1:45275974-45276464	GM12878	blood:	n/a	n/a
11	SPI1	chr1:45276112-45276457	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:45270657-45276553	K562	blood:	n/a	n/a
13	POLR2A	chr1:45272201-45276585	GM12891	blood:	n/a	n/a
14	EBF1	chr1:45274898-45276561	GM12878	blood:	n/a	n/a
15	NFIC	chr1:45275539-45276541	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr1:45272161-45276552	GM12892	blood:	n/a	n/a
17	POLR2A	chr1:45270864-45276511	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:45272275-45276529	MCF10A-Er-Src	breast:	n/a	n/a
19	EBF1	chr1:45275845-45276468	GM12878	blood:	n/a	n/a
20	RELA	chr1:45275095-45276512	GM15510	blood:	n/a	n/a
21	POLR2A	chr1:45272557-45276628	HUVEC	blood vessel:	n/a	n/a
22	RELA	chr1:45275079-45276508	GM10847	blood:	n/a	n/a
23	POLR2A	chr1:45275771-45276491	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:45274366-45276542	GM12891	blood:	n/a	n/a
25	EBF1	chr1:45275932-45276499	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:45271639-45276486	HL-60	blood:	n/a	n/a
27	POU2F2	chr1:45275627-45276441	GM12878	blood:	n/a	n/a
28	ELF1	chr1:45275677-45276439	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:45272231-45276688	SK-N-SH	brain:	n/a	n/a
30	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
31	POLR2A	chr1:45272349-45276663	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr1:45270671-45276445	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr1:45270669-45276523	GM12878	blood:	n/a	n/a
34	IRF4	chr1:45276018-45276558	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:45272457-45276576	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr1:45276212-45276576	Hela-S3	cervix:	n/a	n/a
37	SPI1	chr1:45276090-45276447	GM12891	blood:	n/a	n/a
38	POLR2A	chr1:45272237-45276505	HUVEC	blood vessel:	n/a	n/a
39	MAX	chr1:45274816-45276437	GM12878	blood:	n/a	chr1:45275856-45275866
40	POLR2A	chr1:45271526-45276700	GM12892	blood:	n/a	n/a
41	EP300	chr1:45275915-45276440	GM12878	blood:	n/a	n/a
42	WRNIP1	chr1:45276226-45276499	GM12878	blood:	n/a	n/a
43	RELA	chr1:45276006-45276498	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:45276243-45276639	GM12892	blood:	n/a	n/a
45	POLR2A	chr1:45270812-45279067	A549	lung:	n/a	n/a
46	POLR2A	chr1:45276331-45276443	K562	blood:	n/a	n/a
47	TCF3	chr1:45275884-45276487	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:45272451-45276703	HUVEC	blood vessel:	n/a	n/a
49	ATF2	chr1:45275929-45276440	GM12878	blood:	n/a	n/a
50	RELA	chr1:45275993-45276599	GM19099	blood:	n/a	n/a

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	chr1:45273605..45276582-chr1:45986789..45988627,2	K562	blood:
7	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
8	chr1:45272934..45277358-chr1:45964626..45967668,4	K562	blood:
9	chr1:45239942..45244585-chr1:45273690..45277023,5	MCF-7	breast:
10	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:

Variant related genes	Relation type
BTBD19	TF binding region
TCTEX1D4	TF binding region
ENSG00000200169	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000234093	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000142959	Chromatin interaction
ENSG00000200913	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10159318	0.94[CEU][hapmap]
rs1022814	0.94[CEU][hapmap]
rs11211042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11211043	0.87[ASN][1000 genomes]
rs11211052	0.94[CEU][hapmap]
rs11211062	0.94[CEU][hapmap]
rs11211063	0.94[CEU][hapmap]
rs12057238	0.88[CEU][hapmap]
rs12093313	0.94[CEU][hapmap]
rs12095412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12402452	0.94[CEU][hapmap]
rs12402781	0.88[CEU][hapmap]
rs12403201	0.94[CEU][hapmap]
rs12404160	0.90[EUR][1000 genomes]
rs12404244	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12405110	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12405721	0.93[CEU][hapmap]
rs12407290	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs12407565	0.94[CEU][hapmap]
rs12408763	0.80[EUR][1000 genomes]
rs16832249	0.93[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs16832251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16832301	0.94[CEU][hapmap]
rs17390328	0.94[CEU][hapmap]
rs17392632	0.94[CEU][hapmap]
rs17883304	0.93[EUR][1000 genomes]
rs17885815	0.89[EUR][1000 genomes]
rs2102035	0.94[CEU][hapmap]
rs2295996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs263979	0.94[CEU][hapmap]
rs264002	0.94[CEU][hapmap]
rs3738248	0.94[CEU][hapmap]
rs3889352	0.94[CEU][hapmap]
rs3889822	0.94[CEU][hapmap]
rs3923304	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs392410	0.94[CEU][hapmap]
rs4073112	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4082644	0.94[CEU][hapmap]
rs41269085	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs435311	0.94[CEU][hapmap]
rs4520451	0.90[EUR][1000 genomes]
rs4565758	0.93[EUR][1000 genomes]
rs471564	0.94[CEU][hapmap]
rs59803789	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60189524	0.93[EUR][1000 genomes]
rs60766209	0.85[ASN][1000 genomes]
rs608649	0.94[CEU][hapmap]
rs637224	0.94[CEU][hapmap]
rs6657078	0.88[ASN][1000 genomes]
rs6678737	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72674049	0.88[ASN][1000 genomes]
rs72674051	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7515226	0.94[CEU][hapmap]
rs7519592	0.94[CEU][hapmap]
rs7529213	0.94[CEU][hapmap]

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	chr1:45265600-45276600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:45270000-45278200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:45271800-45277400	Weak transcription	Ovary	ovary
4	chr1:45272000-45278000	Enhancers	Primary hematopoietic stem cells	blood
5	chr1:45272400-45276600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:45272400-45276600	Enhancers	Pancreas	Pancrea
7	chr1:45272400-45277600	Enhancers	Primary B cells from peripheral blood	blood
8	chr1:45272600-45276800	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr1:45272600-45277000	Enhancers	Lung	lung
10	chr1:45272800-45276600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:45272800-45277600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:45272800-45278000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:45273000-45278000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:45273400-45278000	Enhancers	Brain Substantia Nigra	brain
15	chr1:45273600-45277600	Enhancers	Gastric	stomach
16	chr1:45273800-45276600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr1:45274000-45278000	Enhancers	Thymus	Thymus
18	chr1:45274200-45279200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr1:45274400-45279000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:45274800-45276600	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr1:45274800-45277000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr1:45274800-45278000	Enhancers	Hela-S3	cervix
23	chr1:45274800-45278200	Weak transcription	Fetal Heart	heart
24	chr1:45274800-45278400	Weak transcription	Fetal Brain Female	brain
25	chr1:45274800-45278600	Enhancers	Brain Angular Gyrus	brain
26	chr1:45274800-45279000	Enhancers	Fetal Thymus	thymus
27	chr1:45275000-45276600	Enhancers	Liver	Liver
28	chr1:45275000-45277600	Enhancers	Right Ventricle	heart
29	chr1:45275000-45278200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:45275000-45278400	Weak transcription	Fetal Brain Male	brain
31	chr1:45275000-45278600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:45275000-45278600	Enhancers	Brain Anterior Caudate	brain
33	chr1:45275000-45278600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:45275000-45278800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:45275000-45279000	Genic enhancers	Placenta	Placenta
36	chr1:45275200-45276600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:45275200-45278200	Enhancers	K562	blood
38	chr1:45275200-45278800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:45275200-45278800	Enhancers	Right Atrium	heart
40	chr1:45275200-45279000	Enhancers	Primary T cells fromperipheralblood	blood
41	chr1:45275200-45279400	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr1:45275400-45276600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:45275400-45276600	Enhancers	Fetal Intestine Large	intestine
44	chr1:45275400-45278000	Enhancers	Fetal Muscle Leg	muscle
45	chr1:45275400-45278200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr1:45275400-45278800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr1:45275400-45278800	Enhancers	Placenta Amnion	Placenta Amnion
48	chr1:45275400-45279200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:45275400-45279200	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr1:45275600-45276600	Genic enhancers	Fetal Stomach	stomach

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