Variant report

Variant	rs1166698
Chromosome Location	chr1:78392446-78392447
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr1:78392284-78392686	GM12878	blood:	n/a	n/a
2	SPI1	chr1:78392379-78392587	GM12878	blood:	n/a	n/a
3	RUNX3	chr1:78392202-78392646	GM12878	blood:	n/a	n/a
4	PML	chr1:78392180-78392811	GM12878	blood:	n/a	n/a
5	TBL1XR1	chr1:78392315-78392510	K562	blood:	n/a	n/a
6	UBTF	chr1:78392371-78392484	K562	blood:	n/a	n/a
7	JUND	chr1:78392395-78392563	K562	blood:	n/a	n/a
8	NRF1	chr1:78392412-78392477	K562	blood:	n/a	n/a
9	IRF1	chr1:78392200-78392697	K562	blood:	n/a	n/a
10	TBL1XR1	chr1:78392308-78392598	GM12878	blood:	n/a	n/a
11	EP300	chr1:78392025-78392519	K562	blood:	n/a	n/a
12	NFIC	chr1:78392142-78392721	GM12878	blood:	n/a	n/a
13	RCOR1	chr1:78392252-78392568	K562	blood:	n/a	n/a
14	MEF2A	chr1:78392157-78392619	GM12878	blood:	n/a	n/a
15	BCLAF1	chr1:78392100-78392692	GM12878	blood:	n/a	n/a
16	MYC	chr1:78392218-78392608	K562	blood:	n/a	n/a
17	ZNF143	chr1:78392399-78392548	GM12878	blood:	n/a	n/a
18	BHLHE40	chr1:78392312-78392623	GM12878	blood:	n/a	n/a
19	SPI1	chr1:78392330-78392607	GM12891	blood:	n/a	n/a
20	TAF1	chr1:78392306-78392625	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78392441..78395302-chr1:78399570..78403440,3	K562	blood:

No data

Variant related genes	Relation type
NEXN	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11162408	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28735417	0.85[CHB][hapmap];0.82[TSI][hapmap]
rs6424659	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs6699769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs6702939	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs7514180	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7537908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9726525	0.86[CHB][hapmap];1.00[JPT][hapmap]

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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1166698	NEXN	Cis_1M	lymphoblastoid	RTeQTL
rs1166698	TYW3	cis	cerebellum	SCAN
rs1166698	NEXN	cis	lymphoblastoid	seeQTL
rs1166698	DNAJB4	Cis_1M	lymphoblastoid	RTeQTL
rs1166698	NEXN	cis	multi-tissue	Pritchard
rs1166698	DNAJB4	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78356200-78408600	Weak transcription	HMEC	breast
2	chr1:78356400-78396000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:78367000-78407000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:78371600-78413000	Weak transcription	Psoas Muscle	Psoas
5	chr1:78372800-78418600	Weak transcription	Pancreas	Pancrea
6	chr1:78381600-78395200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:78382200-78407400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:78382200-78408000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:78382400-78394000	Strong transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:78382400-78405600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:78382800-78395800	Weak transcription	NHDF-Ad	bronchial
12	chr1:78383000-78400000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:78383600-78418600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:78383800-78404000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:78384000-78395400	Weak transcription	Fetal Heart	heart
16	chr1:78384400-78395400	Weak transcription	Right Ventricle	heart
17	chr1:78384600-78396400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:78384600-78406000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:78385200-78400000	Weak transcription	Fetal Intestine Large	intestine
20	chr1:78385600-78396400	Weak transcription	Ovary	ovary
21	chr1:78387600-78395000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:78387600-78395200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:78387600-78399400	Weak transcription	Fetal Intestine Small	intestine
24	chr1:78387800-78412600	Weak transcription	Fetal Brain Male	brain
25	chr1:78388600-78393200	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:78388600-78416800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:78388800-78410000	Strong transcription	HSMMtube	muscle
28	chr1:78389000-78395600	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:78389000-78414600	Strong transcription	NH-A	brain
30	chr1:78389200-78400200	Weak transcription	Gastric	stomach
31	chr1:78389400-78394800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:78389800-78394000	Strong transcription	Fetal Lung	lung
33	chr1:78390200-78399400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:78390200-78409800	Weak transcription	NHEK	skin
35	chr1:78390600-78392600	Weak transcription	Fetal Stomach	stomach
36	chr1:78390600-78393000	Weak transcription	Aorta	Aorta
37	chr1:78391200-78401000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:78391200-78407000	Weak transcription	Fetal Kidney	kidney
39	chr1:78391200-78407200	Strong transcription	Osteobl	bone
40	chr1:78391400-78404000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:78391600-78403400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:78391800-78392800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:78391800-78393000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:78391800-78393200	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr1:78391800-78393400	Strong transcription	HUVEC	blood vessel
46	chr1:78391800-78393600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:78391800-78393800	Strong transcription	Left Ventricle	heart
48	chr1:78391800-78394000	Flanking Active TSS	Dnd41	blood
49	chr1:78391800-78398800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:78392000-78392600	Active TSS	Primary monocytes fromperipheralblood	blood

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