Variant report

Variant	rs10798778
Chromosome Location	chr1:180536954-180536955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180524885..180529280-chr1:180535382..180538296,3	MCF-7	breast:
2	chr1:180535652..180538329-chr1:180539867..180543816,3	K562	blood:
3	chr1:180513656..180516816-chr1:180534714..180539709,4	K562	blood:
4	chr1:180536800..180538673-chr1:180600367..180602575,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236719	Chromatin interaction
ENSG00000143324	Chromatin interaction
ENSG00000266683	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10914042	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10914043	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10914044	0.82[ASN][1000 genomes]
rs10914046	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10914047	0.82[ASN][1000 genomes]
rs2331545	0.95[CHB][hapmap];0.87[CHD][hapmap];0.80[JPT][hapmap];0.91[ASN][1000 genomes]
rs34569745	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4083947	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6678305	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7527034	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7532437	0.83[ASN][1000 genomes]
rs7542168	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9943120	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats 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	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv947137	chr1:180531647-180537166	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10798778	Contig51737_RC	trans	multi-tissue	Pritchard
rs10798778	NPHS2	cis	cerebellum	SCAN
rs10798778	C1orf220	cis	parietal	SCAN
rs10798778	LHX4	cis	Liver	GTEx
rs10798778	ANGPTL1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180531400-180537400	Enhancers	Fetal Brain Male	brain
2	chr1:180532600-180537000	Weak transcription	Aorta	Aorta
3	chr1:180532600-180539800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:180532600-180540400	Weak transcription	A549	lung
5	chr1:180532800-180539400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:180532800-180539600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:180532800-180539600	Weak transcription	HMEC	breast
8	chr1:180533000-180538600	Weak transcription	Osteobl	bone
9	chr1:180534000-180539400	Weak transcription	K562	blood
10	chr1:180534600-180537000	Enhancers	HUVEC	blood vessel
11	chr1:180535000-180537400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:180535000-180539400	Weak transcription	Fetal Heart	heart
13	chr1:180535000-180540400	Weak transcription	Right Ventricle	heart
14	chr1:180535400-180539600	Weak transcription	HSMMtube	muscle
15	chr1:180535400-180540800	Weak transcription	Pancreas	Pancrea
16	chr1:180536200-180539000	Weak transcription	Left Ventricle	heart
17	chr1:180536200-180543200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:180536400-180537200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr1:180536600-180537000	Flanking Active TSS	Fetal Brain Female	brain
20	chr1:180536600-180537200	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr1:180536600-180537400	Enhancers	Fetal Intestine Large	intestine
22	chr1:180536600-180537400	Enhancers	HepG2	liver
23	chr1:180536800-180537000	Enhancers	Psoas Muscle	Psoas
24	chr1:180536800-180537200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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