Variant report

Variant	rs17100850
Chromosome Location	chr1:78106865-78106866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78104461..78107846-chr1:78109703..78112560,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP33-1	chr1:78106639-78107131	NONHSAT004036

Variant related genes	Relation type
ENSG00000243437	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11800652	1.00[CEU][hapmap]
rs11810135	1.00[CEU][hapmap]
rs12564592	1.00[CEU][hapmap]
rs12564604	1.00[CEU][hapmap]
rs12568374	1.00[CEU][hapmap]
rs12568376	1.00[CEU][hapmap]
rs12569104	1.00[CEU][hapmap]
rs1353727	1.00[MEX][hapmap]
rs17100774	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]
rs17100789	1.00[MEX][hapmap]
rs17100791	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.87[EUR][1000 genomes]
rs17100941	1.00[MEX][hapmap]
rs17101048	1.00[EUR][1000 genomes]
rs17101052	1.00[EUR][1000 genomes]
rs2245189	1.00[CEU][hapmap]
rs2270539	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2291689	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2291690	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2647491	1.00[MEX][hapmap]
rs3112830	1.00[MEX][hapmap]
rs56325960	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	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
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17100850	NEXN	cis	lymphoblastoid	seeQTL
rs17100850	FUBP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78076400-78113000	Weak transcription	Psoas Muscle	Psoas
2	chr1:78089800-78107400	Strong transcription	Primary B cells from cord blood	blood
3	chr1:78090200-78107400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr1:78092800-78107400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:78094200-78107400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:78094400-78107200	Strong transcription	Fetal Thymus	thymus
7	chr1:78094800-78113600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:78096200-78110400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:78096200-78111000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:78098400-78113400	Weak transcription	Pancreas	Pancrea
11	chr1:78098400-78116800	Weak transcription	Right Ventricle	heart
12	chr1:78098600-78110600	Weak transcription	Lung	lung
13	chr1:78098600-78111400	Weak transcription	Brain Germinal Matrix	brain
14	chr1:78098600-78113200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:78098800-78108000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:78098800-78110200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:78098800-78110600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:78099000-78108000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:78099000-78108200	Weak transcription	Colonic Mucosa	Colon
20	chr1:78099000-78110200	Weak transcription	Placenta	Placenta
21	chr1:78099000-78110600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:78099000-78110600	Weak transcription	Esophagus	oesophagus
23	chr1:78099000-78110600	Weak transcription	Ovary	ovary
24	chr1:78099000-78110600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:78099000-78110600	Weak transcription	Thymus	Thymus
26	chr1:78099000-78111600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:78099000-78112600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:78099000-78113800	Weak transcription	Fetal Brain Male	brain
29	chr1:78099000-78113800	Weak transcription	Spleen	Spleen
30	chr1:78099000-78147200	Weak transcription	Gastric	stomach
31	chr1:78099200-78110400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:78099200-78110400	Weak transcription	Fetal Brain Female	brain
33	chr1:78099200-78110600	Weak transcription	Left Ventricle	heart
34	chr1:78099200-78110600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:78099200-78114000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:78099200-78115000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:78099200-78120800	Weak transcription	Small Intestine	intestine
38	chr1:78099200-78132400	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:78099600-78108800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:78099600-78110400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:78099600-78116800	Weak transcription	Aorta	Aorta
42	chr1:78100400-78110600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr1:78100600-78110600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:78100600-78111600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:78100800-78110200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr1:78100800-78110400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:78100800-78110400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:78100800-78115800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:78100800-78116600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr1:78100800-78133200	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links