Variant report

Variant	rs4073112
Chromosome Location	chr1:45278094-45278095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45276857-45278226	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr1:45276824-45278100	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:45276887-45279616	IMR90	lung:	n/a	n/a
4	POLR2A	chr1:45270812-45279067	A549	lung:	n/a	n/a
5	POLR2A	chr1:45277495-45278117	GM12891	blood:	n/a	n/a
6	POLR2A	chr1:45276872-45278117	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45190324..45200952-chr1:45272085..45288310,59	MCF-7	breast:
2	chr1:45193356..45196908-chr1:45277414..45280591,3	MCF-7	breast:
3	chr1:45184399..45189674-chr1:45270870..45279135,15	MCF-7	breast:
4	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
5	chr1:45241279..45243837-chr1:45275916..45278923,3	MCF-7	breast:
6	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
7	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:

No data

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

Extended variants
information (count: 66 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10159318	0.94[CEU][hapmap]
rs1022814	0.94[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap]
rs11211042	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.84[YRI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211043	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11211052	0.94[CEU][hapmap]
rs11211062	0.94[CEU][hapmap]
rs11211063	0.94[CEU][hapmap]
rs12057238	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs12093313	0.94[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs12095412	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs12402452	0.94[CEU][hapmap]
rs12402781	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs12403201	0.94[CEU][hapmap]
rs12404160	0.98[EUR][1000 genomes]
rs12404244	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405110	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12405721	0.93[CEU][hapmap]
rs12407290	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12407565	0.94[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap]
rs12408763	0.82[EUR][1000 genomes]
rs16832249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16832251	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16832301	0.94[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs17390328	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17392632	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17883304	0.95[EUR][1000 genomes]
rs17885815	0.96[EUR][1000 genomes]
rs2102035	0.93[CEU][hapmap]
rs2295996	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs263979	0.94[CEU][hapmap]
rs264002	0.94[CEU][hapmap];0.87[GIH][hapmap]
rs3738248	0.93[CEU][hapmap]
rs3795718	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3889352	0.94[CEU][hapmap]
rs3889822	0.94[CEU][hapmap]
rs3923304	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs392410	0.93[CEU][hapmap]
rs4082644	0.94[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap]
rs41269085	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs435311	0.94[CEU][hapmap]
rs4520451	0.98[EUR][1000 genomes]
rs4565758	0.95[EUR][1000 genomes]
rs471564	0.94[CEU][hapmap]
rs59803789	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60189524	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60766209	0.89[ASN][1000 genomes]
rs608649	0.94[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs637224	0.94[CEU][hapmap]
rs6657078	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6678737	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72674049	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72674051	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7515226	0.94[CEU][hapmap]
rs7519592	0.94[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap]
rs7529213	0.94[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4073112	C1orf84	cis	parietal	SCAN
rs4073112	EBNA1BP2	cis	cerebellum	SCAN
rs4073112	ZNF691	cis	parietal	SCAN
rs4073112	TIE1	cis	cerebellum	SCAN
rs4073112	CDC20	cis	cerebellum	SCAN
rs4073112	SNORD55	cis	cerebellum	SCAN

Chromatin state (count:124 , 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	chr1:45274200-45279200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr1:45274400-45279000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:45274800-45278200	Weak transcription	Fetal Heart	heart
5	chr1:45274800-45278400	Weak transcription	Fetal Brain Female	brain
6	chr1:45274800-45278600	Enhancers	Brain Angular Gyrus	brain
7	chr1:45274800-45279000	Enhancers	Fetal Thymus	thymus
8	chr1:45275000-45278200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:45275000-45278400	Weak transcription	Fetal Brain Male	brain
10	chr1:45275000-45278600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:45275000-45278600	Enhancers	Brain Anterior Caudate	brain
12	chr1:45275000-45278600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:45275000-45278800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:45275000-45279000	Genic enhancers	Placenta	Placenta
15	chr1:45275200-45278200	Enhancers	K562	blood
16	chr1:45275200-45278800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:45275200-45278800	Enhancers	Right Atrium	heart
18	chr1:45275200-45279000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr1:45275200-45279400	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr1:45275400-45278200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr1:45275400-45278800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:45275400-45278800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr1:45275400-45279200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:45275400-45279200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr1:45275600-45278600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:45275600-45278600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:45275600-45278600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:45275600-45278600	Weak transcription	Brain Germinal Matrix	brain
29	chr1:45275600-45278800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:45275800-45278600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:45275800-45278600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr1:45275800-45278800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:45275800-45278800	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr1:45275800-45279000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:45275800-45279000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:45275800-45279200	Weak transcription	Fetal Kidney	kidney
37	chr1:45275800-45281600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:45276000-45278400	Enhancers	Brain Cingulate Gyrus	brain
39	chr1:45276000-45278600	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr1:45276000-45278800	Enhancers	Duodenum Mucosa	Duodenum
41	chr1:45276000-45278800	Weak transcription	Psoas Muscle	Psoas
42	chr1:45276000-45279000	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr1:45276000-45279200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:45276000-45279800	Enhancers	NHDF-Ad	bronchial
45	chr1:45276000-45280600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:45276200-45278200	Genic enhancers	HMEC	breast
47	chr1:45276200-45278400	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr1:45276200-45278600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:45276200-45278600	Enhancers	Brain Hippocampus Middle	brain
50	chr1:45276200-45278600	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links