Variant report

Variant	rs2488770
Chromosome Location	chr1:112934517-112934518
allele	C/T
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 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	chr1:112931958..112934579-chr1:113156530..113159050,3	MCF-7	breast:
11	chr1:112933576..112940137-chr1:113246857..113251993,14	MCF-7	breast:
12	chr1:112932569..112934553-chr1:113008416..113009436,11	K562	blood:
13	chr1:112930309..112940640-chr1:113155859..113164847,24	MCF-7	breast:
14	chr1:112934517..112936780-chr1:113213941..113216268,2	MCF-7	breast:
15	chr1:112932253..112935009-chr1:112937010..112939988,4	MCF-7	breast:

No data

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

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11102471	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
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]
rs1419041	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891705	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891707	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2488762	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2488763	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2488765	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488766	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488768	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488769	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492501	0.87[ASN][1000 genomes]
rs2492502	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492503	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492504	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999472	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240532	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7415832	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[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	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
rs2488770	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	chr1:112933400-112934600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:112933400-112934600	Active TSS	Fetal Brain Female	brain
3	chr1:112933800-112934600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr1:112933800-112934600	Flanking Active TSS	Rectal Smooth Muscle	rectum
5	chr1:112934000-112934800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:112934000-112936000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr1:112934000-112936200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:112934000-112937200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:112934000-112937200	Weak transcription	Liver	Liver
10	chr1:112934000-112937600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:112934000-112938000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:112934000-112938000	Weak transcription	Pancreas	Pancrea
13	chr1:112934000-112938200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:112934200-112934600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:112934200-112934600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:112934200-112934600	Enhancers	Fetal Intestine Small	intestine
17	chr1:112934200-112935400	Enhancers	Fetal Intestine Large	intestine
18	chr1:112934200-112935600	Weak transcription	GM12878-XiMat	blood
19	chr1:112934200-112936000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr1:112934200-112936200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:112934200-112936200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:112934200-112936200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:112934200-112936200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:112934200-112936200	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:112934200-112936200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:112934200-112936200	Weak transcription	HSMMtube	muscle
27	chr1:112934200-112936200	Enhancers	Osteobl	bone
28	chr1:112934200-112936400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:112934200-112936400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:112934200-112936600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:112934200-112936600	Weak transcription	Right Atrium	heart
32	chr1:112934200-112936800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:112934200-112936800	Weak transcription	Brain Angular Gyrus	brain
34	chr1:112934200-112937000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr1:112934200-112937000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:112934200-112937000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:112934200-112937000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr1:112934200-112937000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:112934200-112937000	Weak transcription	Brain Anterior Caudate	brain
40	chr1:112934200-112937000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:112934200-112937000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr1:112934200-112937200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:112934200-112937200	Weak transcription	Ovary	ovary
44	chr1:112934200-112937200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:112934200-112937200	Weak transcription	Spleen	Spleen
46	chr1:112934200-112937600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr1:112934200-112937600	Weak transcription	Brain Germinal Matrix	brain
48	chr1:112934200-112937600	Weak transcription	Esophagus	oesophagus
49	chr1:112934200-112937600	Weak transcription	Right Ventricle	heart
50	chr1:112934200-112938000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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