Variant report

Variant	rs2273165
Chromosome Location	chr1:94341267-94341268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:94333938-94341380	K562	blood:	n/a	n/a
2	MAFK	chr1:94341236-94341418	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:94332079..94335914-chr1:94341026..94344306,4	K562	blood:
2	chr1:94340857..94342610-chr1:94343304..94345726,2	K562	blood:
3	chr1:93811555..93814046-chr1:94339710..94342283,2	K562	blood:
4	chr1:94340990..94343514-chr1:94369991..94373741,3	K562	blood:
5	chr1:94340793..94342610-chr1:94344226..94345915,2	K562	blood:
6	chr1:94340612..94342966-chr1:94406740..94409371,2	K562	blood:

No data

Variant related genes	Relation type
DNTTIP2	TF binding region
ENSG00000067334	Chromatin interaction
ENSG00000223745	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1051394	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165021	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165022	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165023	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165025	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11165026	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12023010	0.81[AFR][1000 genomes]
rs12029548	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12029637	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12029670	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12041975	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12097812	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12758972	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2092698	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2092699	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2103784	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2143992	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2273166	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2391315	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2391321	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3789459	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789460	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4847191	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4847193	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4847263	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4847264	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664876	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6666633	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6667991	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6681169	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6681265	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6684054	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6697189	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7364663	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7513489	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7513786	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7514828	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7517632	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7518940	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7555136	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7556047	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7556107	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][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	nsv998755	chr1:94294015-94341712	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases
2	esv3325380	chr1:94340814-94342475	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2273165	RP11-488P3.1	cis	lung	GTEx
rs2273165	DNTTIP2	Cis_1M	lymphoblastoid	RTeQTL
rs2273165	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2273165	RP11-488P3.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94322200-94343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:94329800-94343600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:94330600-94343600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:94332400-94342000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:94332800-94341400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:94332800-94341600	Strong transcription	Primary B cells from peripheral blood	blood
7	chr1:94332800-94341600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:94332800-94341800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:94332800-94341800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:94332800-94341800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:94332800-94343200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:94332800-94343200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:94333000-94341600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:94333000-94342000	Strong transcription	Fetal Brain Female	brain
15	chr1:94333200-94341600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr1:94333200-94341600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:94333200-94343200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:94333400-94341600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:94333600-94341800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:94333800-94341600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:94333800-94343000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:94334000-94341600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:94334000-94341600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:94334000-94341600	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:94334000-94341800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:94334000-94341800	Strong transcription	Fetal Kidney	kidney
27	chr1:94334000-94341800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr1:94334000-94342000	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:94334000-94343000	Strong transcription	Fetal Thymus	thymus
30	chr1:94334000-94343400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:94334200-94341600	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr1:94334200-94341600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:94334200-94341600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:94334200-94341600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:94334200-94341600	Strong transcription	Adipose Nuclei	Adipose
36	chr1:94334200-94341600	Strong transcription	Liver	Liver
37	chr1:94334200-94341600	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr1:94334200-94341800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:94334200-94341800	Strong transcription	Brain Germinal Matrix	brain
40	chr1:94334200-94341800	Strong transcription	Rectal Smooth Muscle	rectum
41	chr1:94334200-94342000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:94334200-94343200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr1:94334200-94343200	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr1:94334200-94343200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:94334200-94343200	Strong transcription	Fetal Muscle Leg	muscle
46	chr1:94334200-94343400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:94334200-94343400	Strong transcription	Placenta	Placenta
48	chr1:94334400-94341600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:94334400-94341800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:94334400-94341800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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