Variant report

Variant	rs7079700
Chromosome Location	chr10:45478681-45478682
allele	G/T
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	chr10:45478564-45478895	HepG2	liver:	n/a	n/a
2	POLR2A	chr10:45475989-45478887	U87	brain:	n/a	n/a
3	POLR2A	chr10:45475995-45478881	U87	brain:	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	chr10:45453318..45455327-chr10:45477856..45480219,2	MCF-7	breast:

Variant related genes	Relation type
C10orf10	TF binding region
RASSF4	TF binding region
ENSG00000273363	Chromatin interaction
ENSG00000224812	Chromatin interaction
ENSG00000107551	Chromatin interaction
ENSG00000165507	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10793574	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11239301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758402	0.84[YRI][hapmap]
rs870957	0.87[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap]
rs871043	0.83[GIH][hapmap];0.88[TSI][hapmap]

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
rs7079700	RASSF4	cis	multi-tissue	Pritchard

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45470800-45479400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr10:45474200-45478800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr10:45474200-45479000	Enhancers	Stomach Mucosa	stomach
4	chr10:45474200-45479000	Enhancers	HUVEC	blood vessel
5	chr10:45474400-45478800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr10:45474400-45480000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr10:45474400-45484000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr10:45474400-45490800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr10:45474400-45490800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr10:45474600-45483000	Enhancers	Ovary	ovary
11	chr10:45474800-45478800	Enhancers	Right Ventricle	heart
12	chr10:45474800-45479000	Enhancers	Left Ventricle	heart
13	chr10:45474800-45482400	Enhancers	Fetal Heart	heart
14	chr10:45474800-45490200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr10:45475000-45479000	Weak transcription	Fetal Brain Female	brain
16	chr10:45475000-45485000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr10:45476200-45480600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr10:45476200-45484600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr10:45476400-45479600	Weak transcription	Brain Germinal Matrix	brain
20	chr10:45476400-45480200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr10:45476400-45480800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr10:45476400-45480800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr10:45476400-45480800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr10:45476400-45481200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr10:45476600-45480400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr10:45476600-45480600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr10:45476600-45480800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr10:45476600-45483800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr10:45476800-45480600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr10:45476800-45480800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr10:45476800-45481000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr10:45476800-45481400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr10:45476800-45484600	Weak transcription	Fetal Thymus	thymus
34	chr10:45476800-45487400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr10:45476800-45491400	Weak transcription	Fetal Kidney	kidney
36	chr10:45477000-45480400	Weak transcription	K562	blood
37	chr10:45477200-45479600	Enhancers	Lung	lung
38	chr10:45477200-45480200	Weak transcription	Fetal Lung	lung
39	chr10:45477200-45481600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr10:45477200-45482000	Genic enhancers	Fetal Muscle Leg	muscle
41	chr10:45477200-45482600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr10:45477400-45479000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:45477400-45481000	Genic enhancers	Pancreas	Pancrea
44	chr10:45477400-45481200	Strong transcription	Fetal Intestine Small	intestine
45	chr10:45477400-45487400	Weak transcription	Fetal Intestine Large	intestine
46	chr10:45477600-45478800	Enhancers	Muscle Satellite Cultured Cells	--
47	chr10:45477600-45478800	Weak transcription	Colon Smooth Muscle	Colon
48	chr10:45477600-45478800	Enhancers	HMEC	breast
49	chr10:45477600-45479600	Weak transcription	GM12878-XiMat	blood
50	chr10:45477600-45480200	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links