Variant report

Variant	rs2999472
Chromosome Location	chr1:112935881-112935882
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:112935622-112939617	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr1:112935669-112936000	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:112935746-112935885	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr1:112935643-112940520	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr1:112935854-112937954	HUVEC	blood vessel:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:112934882..112939118-chr1:113160574..113165273,5	K562	blood:
2	chr1:112933540..112936487-chr15:65596201..65598326,2	K562	blood:
3	chr1:112932411..112934354-chr1:112934374..112936000,2	MCF-7	breast:
4	chr1:112935217..112937989-chr1:113105345..113107131,2	K562	blood:
5	chr1:112934847..112940551-chr1:113160058..113165450,12	MCF-7	breast:
6	chr1:112935506..112938750-chr1:113247926..113251541,4	MCF-7	breast:
7	chr1:112934882..112937734-chr1:113160574..113162558,3	K562	blood:
8	chr1:112934468..112938679-chr1:113215370..113218926,7	MCF-7	breast:
9	chr1:112934954..112937732-chr1:113156801..113159593,3	MCF-7	breast:
10	chr1:112930750..112936540-chr1:113240694..113246273,6	MCF-7	breast:
11	chr1:112933576..112940137-chr1:113246857..113251993,14	MCF-7	breast:
12	chr1:112930309..112940640-chr1:113155859..113164847,24	MCF-7	breast:
13	chr1:112935857..112936857-chr1:113008833..113009341,2	MCF-7	breast:
14	chr1:112934517..112936780-chr1:113213941..113216268,2	MCF-7	breast:
15	chr1:112935548..112944315-chr1:113002393..113010397,28	MCF-7	breast:

No data

Variant related genes	Relation type
CTTNBP2NL	TF binding region
ENSG00000200156	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000134245	Chromatin interaction
ENSG00000155363	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1018712	0.84[CEU][hapmap]
rs11102471	0.92[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1177812	0.83[CEU][hapmap]
rs12080074	0.81[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];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1475710	0.84[CEU][hapmap]
rs1759689	0.84[CEU][hapmap]
rs1759692	0.86[CEU][hapmap]
rs1777608	0.84[CEU][hapmap]
rs1891705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891707	0.87[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2483328	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs2488758	0.84[CEU][hapmap]
rs2488762	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2488763	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2488765	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488766	0.99[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];0.99[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];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488770	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488786	1.00[YRI][hapmap]
rs2488787	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs2492501	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs2492502	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]
rs2492503	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492504	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492507	0.83[CEU][hapmap]
rs2492512	0.84[CEU][hapmap]
rs2492513	0.84[CEU][hapmap]
rs2492534	0.84[CEU][hapmap]
rs4240532	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7415832	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7541222	0.84[CEU][hapmap]

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	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
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2999472	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	chr1:112934000-112936000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr1:112934000-112936200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:112934000-112937200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:112934000-112937200	Weak transcription	Liver	Liver
5	chr1:112934000-112937600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:112934000-112938000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:112934000-112938000	Weak transcription	Pancreas	Pancrea
8	chr1:112934000-112938200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:112934200-112936000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr1:112934200-112936200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:112934200-112936200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr1:112934200-112936200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:112934200-112936200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:112934200-112936200	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:112934200-112936200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:112934200-112936200	Weak transcription	HSMMtube	muscle
17	chr1:112934200-112936200	Enhancers	Osteobl	bone
18	chr1:112934200-112936400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:112934200-112936400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:112934200-112936600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:112934200-112936600	Weak transcription	Right Atrium	heart
22	chr1:112934200-112936800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:112934200-112936800	Weak transcription	Brain Angular Gyrus	brain
24	chr1:112934200-112937000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:112934200-112937000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:112934200-112937000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:112934200-112937000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:112934200-112937000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:112934200-112937000	Weak transcription	Brain Anterior Caudate	brain
30	chr1:112934200-112937000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:112934200-112937000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:112934200-112937200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:112934200-112937200	Weak transcription	Ovary	ovary
34	chr1:112934200-112937200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:112934200-112937200	Weak transcription	Spleen	Spleen
36	chr1:112934200-112937600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:112934200-112937600	Weak transcription	Brain Germinal Matrix	brain
38	chr1:112934200-112937600	Weak transcription	Esophagus	oesophagus
39	chr1:112934200-112937600	Weak transcription	Right Ventricle	heart
40	chr1:112934200-112938000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:112934200-112938000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:112934200-112938000	Weak transcription	Gastric	stomach
43	chr1:112934200-112938200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:112934400-112936000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:112934400-112936000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:112934400-112936000	Weak transcription	Stomach Mucosa	stomach
47	chr1:112934400-112936000	Weak transcription	HSMM	muscle
48	chr1:112934400-112936200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:112934400-112936200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:112934400-112936200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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