Variant report

Variant	rs2492502
Chromosome Location	chr1:112934790-112934791
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:112933540..112936487-chr15:65596201..65598326,2	K562	blood:
2	chr1:112933690..112935205-chr1:113216941..113219249,2	K562	blood:
3	chr1:112932322..112935119-chr1:113174212..113176500,2	K562	blood:
4	chr1:112932411..112934354-chr1:112934374..112936000,2	MCF-7	breast:
5	chr1:112933482..112935599-chr1:113004006..113005580,2	K562	blood:
6	chr1:112933484..112935297-chr1:113006958..113009853,3	MCF-7	breast:
7	chr1:112932104..112935218-chr1:113248160..113251323,3	MCF-7	breast:
8	chr1:112934468..112938679-chr1:113215370..113218926,7	MCF-7	breast:
9	chr1:112930750..112936540-chr1:113240694..113246273,6	MCF-7	breast:
10	chr1:112933576..112940137-chr1:113246857..113251993,14	MCF-7	breast:
11	chr1:112930309..112940640-chr1:113155859..113164847,24	MCF-7	breast:
12	chr1:112934517..112936780-chr1:113213941..113216268,2	MCF-7	breast:
13	chr1:112932253..112935009-chr1:112937010..112939988,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000155363	Chromatin interaction
ENSG00000134245	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000143079	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000116489	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1018712	0.83[CEU][hapmap]
rs11102471	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1177812	0.83[CEU][hapmap]
rs12080074	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12138024	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412931	0.83[CEU][hapmap]
rs1419041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1475710	0.83[CEU][hapmap]
rs1759689	0.83[CEU][hapmap]
rs1759692	0.86[CEU][hapmap]
rs1777608	0.83[CEU][hapmap]
rs1891705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891707	0.87[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2483328	0.83[CEU][hapmap]
rs2488758	0.83[CEU][hapmap]
rs2488762	0.91[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2488763	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2488765	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488768	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]
rs2488769	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]
rs2488770	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488787	0.83[CEU][hapmap]
rs2492501	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs2492503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492507	0.82[CEU][hapmap]
rs2492512	0.83[CEU][hapmap]
rs2492513	0.83[CEU][hapmap]
rs2492534	0.83[CEU][hapmap]
rs2999472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240532	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7415832	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7541222	0.83[CEU][hapmap]

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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2492502	CTTNBP2NL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112934000-112934800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:112934000-112936000	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr1:112934000-112936200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:112934000-112937200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:112934000-112937200	Weak transcription	Liver	Liver
6	chr1:112934000-112937600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:112934000-112938000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:112934000-112938000	Weak transcription	Pancreas	Pancrea
9	chr1:112934000-112938200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:112934200-112935400	Enhancers	Fetal Intestine Large	intestine
11	chr1:112934200-112935600	Weak transcription	GM12878-XiMat	blood
12	chr1:112934200-112936000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr1:112934200-112936200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:112934200-112936200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:112934200-112936200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:112934200-112936200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:112934200-112936200	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:112934200-112936200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:112934200-112936200	Weak transcription	HSMMtube	muscle
20	chr1:112934200-112936200	Enhancers	Osteobl	bone
21	chr1:112934200-112936400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:112934200-112936400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:112934200-112936600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:112934200-112936600	Weak transcription	Right Atrium	heart
25	chr1:112934200-112936800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:112934200-112936800	Weak transcription	Brain Angular Gyrus	brain
27	chr1:112934200-112937000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:112934200-112937000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:112934200-112937000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:112934200-112937000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:112934200-112937000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:112934200-112937000	Weak transcription	Brain Anterior Caudate	brain
33	chr1:112934200-112937000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:112934200-112937000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr1:112934200-112937200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:112934200-112937200	Weak transcription	Ovary	ovary
37	chr1:112934200-112937200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:112934200-112937200	Weak transcription	Spleen	Spleen
39	chr1:112934200-112937600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:112934200-112937600	Weak transcription	Brain Germinal Matrix	brain
41	chr1:112934200-112937600	Weak transcription	Esophagus	oesophagus
42	chr1:112934200-112937600	Weak transcription	Right Ventricle	heart
43	chr1:112934200-112938000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:112934200-112938000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:112934200-112938000	Weak transcription	Gastric	stomach
46	chr1:112934200-112938200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:112934400-112934800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:112934400-112934800	Enhancers	Muscle Satellite Cultured Cells	--
49	chr1:112934400-112934800	Enhancers	Stomach Smooth Muscle	stomach
50	chr1:112934400-112934800	Active TSS	HMEC	breast

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