Variant report

Variant	rs884879
Chromosome Location	chr10:45461114-45461115
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	chr10:45457577-45464667	GM12878	blood:	n/a	n/a
2	POLR2A	chr10:45458760-45462324	GM12891	blood:	n/a	n/a
3	POLR2A	chr10:45460916-45462344	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:45460845-45462395	GM12878	blood:	n/a	n/a
5	PAX5	chr10:45461091-45462325	GM12878	blood:	n/a	n/a
6	RELA	chr10:45460706-45462798	GM12891	blood:	n/a	n/a
7	WRNIP1	chr10:45458658-45462963	GM12878	blood:	n/a	n/a
8	EBF1	chr10:45461012-45461638	GM12878	blood:	n/a	chr10:45461173-45461182 chr10:45461172-45461182
9	POLR2A	chr10:45458224-45466240	HepG2	liver:	n/a	n/a
10	TCF3	chr10:45461080-45461507	GM12878	blood:	n/a	chr10:45461305-45461315
11	RELA	chr10:45461089-45462029	GM18505	blood:	n/a	n/a
12	MTA3	chr10:45460328-45462338	GM12878	blood:	n/a	n/a
13	POLR2A	chr10:45460941-45462455	GM12878	blood:	n/a	n/a
14	CHD1	chr10:45461029-45461712	GM12878	blood:	n/a	n/a
15	TCF7L2	chr10:45460980-45461297	Hela-S3	cervix:	n/a	n/a
16	RELA	chr10:45461006-45462288	GM18951	blood:	n/a	n/a
17	CHD2	chr10:45461049-45461900	GM12878	blood:	n/a	n/a
18	CTCF	chr10:45461080-45461230	GM12871	blood:	n/a	n/a
19	BCLAF1	chr10:45461087-45461907	GM12878	blood:	n/a	chr10:45461162-45461175 chr10:45461777-45461786 chr10:45461707-45461716
20	POLR2A	chr10:45461008-45462190	GM12892	blood:	n/a	n/a
21	EBF1	chr10:45461059-45462433	GM12878	blood:	n/a	chr10:45461173-45461182 chr10:45461172-45461182

No.	Distal block	Cell Line	Cell type
1	chr10:45440452..45443413-chr10:45461070..45463781,2	MCF-7	breast:
2	chr10:45428159..45428765-chr10:45460639..45461384,2	MCF-7	breast:
3	chr10:45458918..45461425-chr10:45473406..45475614,2	MCF-7	breast:
4	chr10:45459948..45462747-chr10:45463776..45467477,3	MCF-7	breast:
5	chr10:45460257..45463291-chr10:45472761..45475493,4	MCF-7	breast:
6	chr10:45427938..45428722-chr10:45460765..45461409,2	MCF-7	breast:

Variant related genes	Relation type
RASSF4	TF binding region
ENSG00000107551	Chromatin interaction
ENSG00000165507	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10793572	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12263146	0.86[CHD][hapmap]
rs1888983	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs3814566	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4948938	0.83[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs59626742	0.80[ASN][1000 genomes]
rs7914175	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1035235	chr10:45442303-45467948	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	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
rs884879	RASSF4	cis	multi-tissue	Pritchard

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45455400-45462800	Flanking Active TSS	GM12878-XiMat	blood
2	chr10:45455600-45462600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:45455600-45465200	Enhancers	Fetal Thymus	thymus
4	chr10:45455600-45465200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr10:45455800-45461400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr10:45455800-45463200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr10:45455800-45464000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr10:45455800-45465600	Weak transcription	Ovary	ovary
9	chr10:45456000-45463000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr10:45456000-45463400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr10:45456200-45463200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr10:45456200-45463600	Weak transcription	Esophagus	oesophagus
13	chr10:45456200-45465000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr10:45456400-45461600	Weak transcription	Osteobl	bone
15	chr10:45456400-45466200	Weak transcription	Aorta	Aorta
16	chr10:45456600-45461400	Enhancers	H1 Cell Line	embryonic stem cell
17	chr10:45456600-45461600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr10:45456600-45461800	Weak transcription	HUVEC	blood vessel
19	chr10:45456600-45462800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr10:45456800-45465200	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr10:45456800-45466600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr10:45457000-45461200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr10:45458000-45462800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr10:45458000-45465000	Enhancers	Primary B cells from cord blood	blood
25	chr10:45458200-45462600	Enhancers	Adipose Nuclei	Adipose
26	chr10:45458200-45465000	Enhancers	Thymus	Thymus
27	chr10:45458400-45461200	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr10:45458400-45461400	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr10:45458400-45461400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr10:45458400-45462000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr10:45458400-45462200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr10:45458400-45463000	Enhancers	Fetal Intestine Large	intestine
33	chr10:45458400-45464200	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr10:45458400-45464400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr10:45458400-45464800	Enhancers	Primary B cells from peripheral blood	blood
36	chr10:45458400-45465800	Enhancers	Psoas Muscle	Psoas
37	chr10:45458600-45462000	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr10:45458800-45461400	Enhancers	Fetal Lung	lung
39	chr10:45458800-45461800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr10:45458800-45463800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr10:45458800-45465200	Enhancers	Spleen	Spleen
42	chr10:45459000-45461600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr10:45459000-45461800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr10:45459000-45464400	Enhancers	Placenta	Placenta
45	chr10:45459000-45465600	Enhancers	Left Ventricle	heart
46	chr10:45459200-45461400	Enhancers	H9 Cell Line	embryonic stem cell
47	chr10:45459200-45461800	Enhancers	Colonic Mucosa	Colon
48	chr10:45459200-45462200	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr10:45459200-45462200	Enhancers	Small Intestine	intestine
50	chr10:45459200-45462800	Weak transcription	Dnd41	blood

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