Variant report

Variant	rs3758401
Chromosome Location	chr10:45476128-45476129
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	MYBL2	chr10:45475803-45477077	HepG2	liver:	n/a	n/a
2	JUND	chr10:45475822-45476507	HepG2	liver:	n/a	chr10:45475955-45475963 chr10:45475956-45475963 chr10:45475955-45475963
3	POLR2A	chr10:45476118-45477994	HUVEC	blood vessel:	n/a	n/a
4	RAD21	chr10:45475899-45476952	HepG2	liver:	n/a	chr10:45475916-45475926 chr10:45476201-45476213
5	RUNX3	chr10:45475595-45476227	GM12878	blood:	n/a	n/a
6	MTA3	chr10:45475774-45476298	GM12878	blood:	n/a	n/a
7	RAD21	chr10:45476008-45476580	HepG2	liver:	n/a	chr10:45476201-45476213
8	TEAD4	chr10:45476050-45476869	HepG2	liver:	n/a	n/a
9	CHD2	chr10:45475712-45476197	GM12878	blood:	n/a	n/a
10	POLR2A	chr10:45475700-45476350	GM12892	blood:	n/a	n/a
11	NFIC	chr10:45475663-45476979	GM12878	blood:	n/a	n/a
12	CHD1	chr10:45475869-45476198	GM12878	blood:	n/a	n/a
13	FOSL2	chr10:45475747-45476574	HepG2	liver:	n/a	chr10:45475955-45475963 chr10:45475956-45475963 chr10:45475955-45475963
14	MXI1	chr10:45475860-45476847	HepG2	liver:	n/a	n/a
15	POLR2A	chr10:45475620-45476218	GM12892	blood:	n/a	n/a
16	HNF4A	chr10:45475991-45476639	HepG2	liver:	n/a	chr10:45476295-45476309 chr10:45476294-45476309 chr10:45476013-45476028 chr10:45476296-45476308 chr10:45476014-45476027 chr10:45476295-45476308 chr10:45476014-45476027 chr10:45476296-45476309 chr10:45476295-45476309 chr10:45476296-45476308 chr10:45476296-45476308 chr10:45476010-45476032
17	BCL3	chr10:45475655-45476179	GM12878	blood:	n/a	chr10:45475857-45475866
18	RCOR1	chr10:45475837-45476806	HepG2	liver:	n/a	n/a
19	NR2F2	chr10:45475763-45476750	HepG2	liver:	n/a	n/a
20	POLR2A	chr10:45476059-45476134	GM12878	blood:	n/a	n/a
21	CTCF	chr10:45476108-45476393	HepG2	liver:	n/a	n/a
22	EP300	chr10:45475706-45476716	HepG2	liver:	n/a	chr10:45476409-45476423
23	MBD4	chr10:45475756-45476668	HepG2	liver:	n/a	n/a
24	POLR2A	chr10:45475326-45477898	HepG2	liver:	n/a	n/a
25	CHD2	chr10:45475754-45476424	HepG2	liver:	n/a	n/a
26	POLR2A	chr10:45475830-45476204	HepG2	liver:	n/a	n/a
27	FOXA1	chr10:45476099-45476645	HepG2	liver:	n/a	n/a
28	POLR2A	chr10:45475836-45476399	HepG2	liver:	n/a	n/a
29	FOXA1	chr10:45475777-45476750	HepG2	liver:	n/a	n/a
30	RAD21	chr10:45476063-45476476	HepG2	liver:	n/a	chr10:45476201-45476213
31	BRCA1	chr10:45476006-45476145	HepG2	liver:	n/a	n/a
32	POLR2A	chr10:45475820-45477448	HepG2	liver:	n/a	n/a
33	ELK1	chr10:45476103-45476165	GM12878	blood:	n/a	n/a
34	NFIC	chr10:45475980-45476673	HepG2	liver:	n/a	n/a
35	ARID3A	chr10:45476116-45477067	HepG2	liver:	n/a	n/a
36	MAX	chr10:45475752-45476914	HepG2	liver:	n/a	chr10:45475954-45475963
37	FOXA1	chr10:45476035-45476743	HepG2	liver:	n/a	n/a
38	MAZ	chr10:45475782-45478019	IMR90	lung:	n/a	chr10:45475954-45475963
39	MAZ	chr10:45475852-45476901	HepG2	liver:	n/a	chr10:45475954-45475963
40	PML	chr10:45475520-45476244	GM12878	blood:	n/a	n/a
41	RUNX3	chr10:45475664-45476181	GM12878	blood:	n/a	n/a
42	POLR2A	chr10:45475837-45476136	GM12878	blood:	n/a	n/a
43	FOXA1	chr10:45476061-45476656	HepG2	liver:	n/a	n/a
44	MAFF	chr10:45476085-45476954	HepG2	liver:	n/a	n/a
45	MTA3	chr10:45475460-45477050	GM12878	blood:	n/a	n/a
46	HEY1	chr10:45475907-45476491	HepG2	liver:	n/a	n/a
47	POLR2A	chr10:45475989-45478887	U87	brain:	n/a	n/a
48	HNF4A	chr10:45475950-45476669	HepG2	liver:	n/a	chr10:45476295-45476309 chr10:45476294-45476309 chr10:45476013-45476028 chr10:45476296-45476308 chr10:45476014-45476027 chr10:45476295-45476308 chr10:45476014-45476027 chr10:45476296-45476309 chr10:45476295-45476309 chr10:45476296-45476308 chr10:45476296-45476308 chr10:45476010-45476032
49	MAFK	chr10:45476095-45477237	HepG2	liver:	n/a	n/a
50	NFIC	chr10:45476006-45477314	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:45472768..45475523-chr10:45475664..45479867,4	MCF-7	breast:
2	chr10:45469560..45475620-chr10:45475961..45481693,7	MCF-7	breast:
3	chr10:45472274..45474352-chr10:45475240..45477414,3	K562	blood:

Variant related genes	Relation type
C10orf10	TF binding region
RASSF4	TF binding region
ENSG00000165507	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11818604	0.92[EUR][1000 genomes]
rs11818623	0.93[EUR][1000 genomes]
rs3740097	0.92[EUR][1000 genomes]
rs3740098	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs3758402	0.91[CEU][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs869156	0.81[CEU][hapmap];0.94[EUR][1000 genomes]
rs882845	0.90[EUR][1000 genomes]
rs883734	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs883735	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs914700	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs914701	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv526734	chr10:45458485-45492054	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3758401	RASSF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45470800-45476400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr10:45470800-45477800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr10:45470800-45479400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr10:45471400-45476600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr10:45471600-45476800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr10:45473000-45477800	Enhancers	Placenta Amnion	Placenta Amnion
7	chr10:45473600-45476400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr10:45473600-45476800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:45473800-45476200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr10:45473800-45476200	Enhancers	Fetal Brain Male	brain
11	chr10:45474000-45476200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:45474000-45476200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr10:45474200-45476400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:45474200-45476400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr10:45474200-45476600	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr10:45474200-45476800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr10:45474200-45476800	Enhancers	Fetal Thymus	thymus
18	chr10:45474200-45477000	Enhancers	Brain Substantia Nigra	brain
19	chr10:45474200-45477200	Enhancers	Fetal Lung	lung
20	chr10:45474200-45477400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:45474200-45478200	Enhancers	Esophagus	oesophagus
22	chr10:45474200-45478200	Enhancers	Psoas Muscle	Psoas
23	chr10:45474200-45478400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr10:45474200-45478800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr10:45474200-45479000	Enhancers	Stomach Mucosa	stomach
26	chr10:45474200-45479000	Enhancers	HUVEC	blood vessel
27	chr10:45474400-45476200	Enhancers	Lung	lung
28	chr10:45474400-45476400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr10:45474400-45476400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:45474400-45476400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr10:45474400-45476400	Enhancers	Brain Germinal Matrix	brain
32	chr10:45474400-45476600	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr10:45474400-45476600	Enhancers	Aorta	Aorta
34	chr10:45474400-45476600	Enhancers	Brain Hippocampus Middle	brain
35	chr10:45474400-45476600	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr10:45474400-45476800	Enhancers	NHDF-Ad	bronchial
37	chr10:45474400-45477200	Enhancers	Primary hematopoietic stem cells	blood
38	chr10:45474400-45477400	Enhancers	Brain Angular Gyrus	brain
39	chr10:45474400-45477400	Enhancers	Pancreas	Pancrea
40	chr10:45474400-45477400	Flanking Active TSS	HepG2	liver
41	chr10:45474400-45477600	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr10:45474400-45477600	Enhancers	GM12878-XiMat	blood
43	chr10:45474400-45478000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr10:45474400-45478200	Enhancers	Fetal Stomach	stomach
45	chr10:45474400-45478400	Enhancers	Right Atrium	heart
46	chr10:45474400-45478600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr10:45474400-45478800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr10:45474400-45480000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr10:45474400-45484000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr10:45474400-45490800	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links