Variant report

Variant	rs2060743
Chromosome Location	chr2:39101885-39101886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr2:39101863-39104341	SK-N-SH	brain:	n/a	chr2:39103127-39103142 chr2:39102329-39102338

No.	Distal block	Cell Line	Cell type
1	chr2:38976877..38979785-chr2:39100480..39105632,13	K562	blood:
2	chr2:38973415..38975366-chr2:39100938..39103537,2	K562	blood:
3	chr2:39092323..39097069-chr2:39100019..39103136,5	MCF-7	breast:
4	chr2:38976936..38979845-chr2:39101241..39105632,7	K562	blood:

Variant related genes	Relation type
MORN2	TF binding region
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000163214	Chromatin interaction

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

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

rs_ID	r²[population]
rs1010858	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779923	0.89[CHB][hapmap]
rs11124655	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11681583	0.84[EUR][1000 genomes]
rs11689954	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12617734	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12712625	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs12712627	0.82[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12712628	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13029388	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs1901289	0.88[CHB][hapmap]
rs2060744	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2373473	0.86[CEU][hapmap];0.83[CHB][hapmap];0.91[EUR][1000 genomes]
rs3099942	0.81[CHB][hapmap]
rs3099943	0.86[EUR][1000 genomes]
rs3099945	0.82[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs3099946	0.92[EUR][1000 genomes]
rs3099948	0.89[EUR][1000 genomes]
rs3099949	0.89[EUR][1000 genomes]
rs3099959	0.94[CHB][hapmap]
rs3112170	0.88[EUR][1000 genomes]
rs3112171	0.81[EUR][1000 genomes]
rs3112172	0.92[EUR][1000 genomes]
rs3923144	0.89[CEU][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4265996	0.84[CHB][hapmap]
rs4670267	0.83[CHB][hapmap]
rs4670899	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4670900	0.92[EUR][1000 genomes]
rs6706091	0.89[CHB][hapmap]
rs6706186	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6738403	0.89[ASN][1000 genomes]
rs6741088	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6744514	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7565111	0.81[YRI][hapmap]
rs9808136	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv2692	chr2:39065768-39111871	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2060743	DHX57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39038800-39102200	Weak transcription	Gastric	stomach
2	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
3	chr2:39080000-39102200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:39081200-39102200	Weak transcription	Right Ventricle	heart
5	chr2:39081200-39102200	Weak transcription	Spleen	Spleen
6	chr2:39081200-39102400	Weak transcription	Pancreas	Pancrea
7	chr2:39088200-39102000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:39089400-39102000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:39089400-39102200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:39089400-39102200	Weak transcription	Ovary	ovary
11	chr2:39089400-39102200	Weak transcription	Small Intestine	intestine
12	chr2:39089600-39102000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:39089600-39102000	Weak transcription	NHLF	lung
14	chr2:39089600-39102400	Weak transcription	Lung	lung
15	chr2:39090000-39102000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:39090000-39102000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:39090200-39102400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:39090600-39102000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr2:39090600-39102000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr2:39090600-39102200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr2:39090800-39102000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:39090800-39102000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr2:39090800-39102000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:39090800-39102000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:39090800-39102000	Weak transcription	Adipose Nuclei	Adipose
26	chr2:39090800-39102000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:39090800-39102000	Weak transcription	HSMMtube	muscle
28	chr2:39090800-39102000	Weak transcription	NHDF-Ad	bronchial
29	chr2:39092000-39102200	Weak transcription	Right Atrium	heart
30	chr2:39092800-39102200	Weak transcription	Psoas Muscle	Psoas
31	chr2:39094200-39102000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:39094200-39102400	Weak transcription	Aorta	Aorta
33	chr2:39094400-39102000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:39094400-39102000	Weak transcription	Liver	Liver
35	chr2:39094400-39102000	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:39094400-39102000	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:39094400-39102200	Weak transcription	HSMM	muscle
38	chr2:39094600-39102000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr2:39094600-39102000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:39094800-39102000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:39094800-39102000	Weak transcription	Thymus	Thymus
42	chr2:39095000-39102000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:39095000-39102000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:39095000-39102200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:39095000-39102200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:39095000-39102200	Weak transcription	Left Ventricle	heart
47	chr2:39095000-39102400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:39095000-39102400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:39095200-39102000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:39095200-39102000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links