Variant report

Variant	rs7525870
Chromosome Location	chr1:78269207-78269208
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs17100758	0.82[AMR][1000 genomes]
rs1968027	0.82[ASN][1000 genomes]
rs278846	0.84[EUR][1000 genomes]
rs278853	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs28735417	0.95[CEU][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap]
rs4121165	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61777140	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9787306	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1004327	chr1:78212804-78352385	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1006600	chr1:78222312-78384009	Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv535011	chr1:78222312-78384009	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7525870	NEXN	Cis_1M	lymphoblastoid	RTeQTL
rs7525870	DNAJB4	cis	parietal	SCAN
rs7525870	NEXN	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78246000-78284200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:78246000-78285600	Weak transcription	Colonic Mucosa	Colon
3	chr1:78246200-78272000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:78246200-78272800	Weak transcription	Psoas Muscle	Psoas
5	chr1:78246200-78279400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:78246200-78279600	Weak transcription	Aorta	Aorta
7	chr1:78246400-78272400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:78246400-78273200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:78246400-78274000	Weak transcription	Fetal Kidney	kidney
10	chr1:78246400-78287400	Weak transcription	Fetal Heart	heart
11	chr1:78246600-78274200	Weak transcription	HMEC	breast
12	chr1:78247400-78278400	Weak transcription	Hela-S3	cervix
13	chr1:78247600-78272400	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:78248600-78288200	Weak transcription	Small Intestine	intestine
15	chr1:78249200-78271400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:78250400-78282400	Weak transcription	NHEK	skin
17	chr1:78250600-78279000	Weak transcription	NHLF	lung
18	chr1:78252000-78272600	Weak transcription	Spleen	Spleen
19	chr1:78252000-78272800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:78252200-78282600	Weak transcription	Right Ventricle	heart
21	chr1:78252200-78315800	Weak transcription	Esophagus	oesophagus
22	chr1:78252800-78272800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:78253000-78272800	Weak transcription	Thymus	Thymus
24	chr1:78253000-78273200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:78253000-78279400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:78253000-78283800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:78253600-78269800	Weak transcription	Brain Germinal Matrix	brain
28	chr1:78254400-78272800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:78254400-78274000	Weak transcription	HSMMtube	muscle
30	chr1:78254400-78287200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:78254600-78271800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:78254600-78272000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:78254600-78272800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:78255000-78272800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:78255400-78269800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:78255600-78271400	Weak transcription	Fetal Brain Female	brain
37	chr1:78256600-78271400	Weak transcription	Lung	lung
38	chr1:78256600-78271600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:78257000-78269400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:78260000-78275400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr1:78260600-78270400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:78260600-78279800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr1:78261000-78273400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:78261600-78275200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:78262200-78270200	Weak transcription	Fetal Intestine Small	intestine
46	chr1:78262600-78270000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:78262600-78271600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:78262800-78270000	Weak transcription	Fetal Stomach	stomach
49	chr1:78262800-78273200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:78262800-78285200	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links