Variant report

Variant	rs2501864
Chromosome Location	chr1:161230480-161230481
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161229889..161232448-chr1:161233494..161236139,3	K562	blood:
2	chr1:161230213..161232749-chr1:161243411..161246206,2	MCF-7	breast:
3	chr1:161229659..161232274-chr1:161282261..161284000,2	K562	blood:

Extended variants
information (count: 3 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs2501879	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2501864	CD1C	cis	parietal	SCAN
rs2501864	TMCC2	trans	parietal	SCAN
rs2501864	MEF2D	cis	parietal	SCAN
rs2501864	LMNA	cis	parietal	SCAN
rs2501864	KCNJ10	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161229200-161230800	Weak transcription	Liver	Liver
2	chr1:161229200-161231200	Weak transcription	Lung	lung
3	chr1:161229400-161234800	Weak transcription	Ovary	ovary
4	chr1:161229800-161230600	Active TSS	Brain Anterior Caudate	brain
5	chr1:161229800-161231000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:161229800-161231400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:161230000-161230600	Flanking Active TSS	Colon Smooth Muscle	Colon
8	chr1:161230000-161230600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
9	chr1:161230000-161230800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
10	chr1:161230200-161230600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
11	chr1:161230200-161230600	Bivalent Enhancer	Fetal Intestine Large	intestine
12	chr1:161230200-161230600	Bivalent Enhancer	Psoas Muscle	Psoas
13	chr1:161230200-161230600	Bivalent Enhancer	HSMM	muscle
14	chr1:161230200-161231400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
15	chr1:161230200-161231400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
16	chr1:161230200-161231400	Bivalent Enhancer	Adipose Nuclei	Adipose
17	chr1:161230200-161231400	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr1:161230200-161231800	Enhancers	Fetal Intestine Small	intestine
19	chr1:161230400-161230600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
20	chr1:161230400-161230600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:161230400-161230600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
22	chr1:161230400-161230600	Bivalent/Poised TSS	Hela-S3	cervix
23	chr1:161230400-161231000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
24	chr1:161230400-161231000	Bivalent Enhancer	HSMMtube	muscle
25	chr1:161230400-161231200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
26	chr1:161230400-161231200	Bivalent Enhancer	Placenta	Placenta
27	chr1:161230400-161231200	Bivalent Enhancer	NHEK	skin
28	chr1:161230400-161231400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
29	chr1:161230400-161231400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:161230400-161231400	Flanking Active TSS	HepG2	liver
31	chr1:161230400-161231600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:161230400-161231600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:161230400-161231800	Enhancers	Esophagus	oesophagus
34	chr1:161230400-161231800	Bivalent Enhancer	Fetal Thymus	thymus
35	chr1:161230400-161231800	Flanking Active TSS	GM12878-XiMat	blood

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