Variant report

Variant	rs17100774
Chromosome Location	chr1:78039216-78039217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1353727	1.00[MEX][hapmap]
rs17100789	1.00[MEX][hapmap]
rs17100791	0.90[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs17100850	0.90[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17100941	1.00[MEX][hapmap]
rs2270539	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291689	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291690	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602939	1.00[MEX][hapmap]
rs2647491	1.00[MEX][hapmap]
rs2803144	1.00[MEX][hapmap]
rs2803149	1.00[MEX][hapmap]
rs3112830	1.00[MEX][hapmap]
rs56259955	0.85[ASN][1000 genomes]
rs7527150	0.88[YRI][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	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	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3337461	chr1:78036000-78153859	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17100774	NEXN	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78006200-78064400	Weak transcription	Stomach Mucosa	stomach
2	chr1:78023200-78050200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:78023400-78046200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:78023800-78048800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:78024600-78048000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr1:78024800-78048400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:78024800-78071000	Weak transcription	Gastric	stomach
8	chr1:78025400-78050600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:78026000-78049400	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr1:78026400-78048800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:78026800-78049200	Weak transcription	Colonic Mucosa	Colon
12	chr1:78027200-78049800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:78028600-78054600	Weak transcription	Esophagus	oesophagus
14	chr1:78029400-78039800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:78029800-78047800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:78029800-78048000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:78029800-78050600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:78030000-78048800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:78030200-78048200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr1:78030200-78048800	Strong transcription	Fetal Intestine Large	intestine
21	chr1:78030200-78049400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:78030400-78047600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr1:78030400-78050400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:78030600-78047800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:78031600-78041800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:78032000-78047200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:78032000-78049000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:78032000-78062800	Weak transcription	Fetal Heart	heart
29	chr1:78032400-78047000	Weak transcription	Fetal Brain Male	brain
30	chr1:78032600-78046600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:78032600-78070800	Weak transcription	Aorta	Aorta
32	chr1:78032800-78041000	Weak transcription	Brain Germinal Matrix	brain
33	chr1:78032800-78070600	Weak transcription	Small Intestine	intestine
34	chr1:78033000-78040200	Weak transcription	Ovary	ovary
35	chr1:78033000-78057000	Weak transcription	Spleen	Spleen
36	chr1:78033000-78057200	Weak transcription	Psoas Muscle	Psoas
37	chr1:78033200-78043200	Weak transcription	Lung	lung
38	chr1:78033200-78072600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:78033400-78040200	Weak transcription	Brain Angular Gyrus	brain
40	chr1:78033400-78057600	Weak transcription	Right Ventricle	heart
41	chr1:78033400-78069600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr1:78033600-78040000	Weak transcription	Primary B cells from cord blood	blood
43	chr1:78033600-78040000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:78033600-78040600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr1:78033600-78044400	Weak transcription	Fetal Kidney	kidney
46	chr1:78033600-78045200	Weak transcription	K562	blood
47	chr1:78033600-78051400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:78033600-78070800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:78033800-78040000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:78033800-78040000	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links