Variant report

Variant	rs10494345
Chromosome Location	chr1:161236636-161236637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161228430..161230750-chr1:161235534..161238135,2	MCF-7	breast:
2	chr1:161227688..161230234-chr1:161234768..161237380,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248485	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11265577	1.00[ASN][1000 genomes]
rs12137529	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]
rs4131775	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4433413	0.86[AMR][1000 genomes];1.00[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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv432986	chr1:161221133-161673682	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv520253	chr1:161234623-161237892	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10494345	JARID2	trans	lymphoblastoid	seeQTL
rs10494345	PFDN2	cis	parietal	SCAN
rs10494345	LRMP	trans	lymphoblastoid	seeQTL
rs10494345	RNF130	trans	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161232600-161237000	Weak transcription	GM12878-XiMat	blood
2	chr1:161233400-161237000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:161234800-161237600	Enhancers	Ovary	ovary
4	chr1:161235000-161237400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:161235200-161237400	Enhancers	Rectal Smooth Muscle	rectum
6	chr1:161235200-161238000	Enhancers	Fetal Stomach	stomach
7	chr1:161235400-161237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:161235600-161237200	Weak transcription	Placenta	Placenta
9	chr1:161235800-161236800	Bivalent Enhancer	Osteobl	bone
10	chr1:161235800-161237000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:161235800-161237200	Enhancers	Brain Anterior Caudate	brain
12	chr1:161235800-161237200	Enhancers	HSMMtube	muscle
13	chr1:161235800-161237400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr1:161235800-161237400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:161235800-161237400	Enhancers	A549	lung
16	chr1:161235800-161237600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr1:161235800-161237600	Enhancers	Fetal Muscle Leg	muscle
18	chr1:161236000-161236800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:161236000-161236800	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr1:161236000-161237200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:161236000-161237200	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr1:161236000-161237200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr1:161236000-161237400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr1:161236000-161237400	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr1:161236000-161237400	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr1:161236000-161237400	Enhancers	Pancreas	Pancrea
27	chr1:161236200-161236800	Enhancers	Right Ventricle	heart
28	chr1:161236200-161237200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr1:161236200-161237200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:161236200-161237400	Enhancers	Left Ventricle	heart
31	chr1:161236400-161236800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:161236400-161237200	Enhancers	Colon Smooth Muscle	Colon
33	chr1:161236600-161236800	Flanking Active TSS	Fetal Heart	heart
34	chr1:161236600-161237600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:161236600-161238000	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr1:161236600-161238200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links