Variant report

Variant	rs2293235
Chromosome Location	chr3:119394168-119394169
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119371437..119373754-chr3:119392688..119396112,3	K562	blood:
2	chr3:119383202..119386543-chr3:119393770..119396267,3	MCF-7	breast:
3	chr3:119215976..119218932-chr3:119393949..119396539,3	K562	blood:
4	chr3:119393569..119396281-chr3:119421855..119424087,2	MCF-7	breast:
5	chr3:119040381..119043387-chr3:119393976..119396207,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POPDC2-4	chr3:119393992-119394424	NONHSAT091401

No data

Variant related genes	Relation type
ENSG00000241155	Chromatin interaction
ENSG00000113845	Chromatin interaction
ENSG00000272662	Chromatin interaction
ENSG00000183833	Chromatin interaction
ENSG00000121577	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12023	0.86[GIH][hapmap];0.88[MEX][hapmap]
rs13062697	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13091305	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13095802	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13323756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17281793	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2319013	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2873788	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs34775086	0.93[GIH][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6773852	0.94[EUR][1000 genomes]
rs6786295	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789504	0.94[EUR][1000 genomes]
rs6792223	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6794067	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6798542	0.92[EUR][1000 genomes]
rs71325390	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9810361	0.94[EUR][1000 genomes]
rs9821541	0.92[EUR][1000 genomes]
rs9822052	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9835803	0.92[ASN][1000 genomes]
rs9837943	0.94[ASN][1000 genomes]
rs9865825	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9873256	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9873609	0.94[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised 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	16 gene(s)	inside rSNPs	diseases
4	nsv1014394	chr3:119360506-119412275	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv460834	chr3:119384163-119458851	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv591390	chr3:119384163-119458851	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2293235	COX17	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119361200-119394400	Weak transcription	Brain Angular Gyrus	brain
2	chr3:119384000-119395000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:119384200-119394400	Weak transcription	Stomach Mucosa	stomach
4	chr3:119384600-119394600	Weak transcription	NH-A	brain
5	chr3:119385400-119394200	Strong transcription	Primary T cells from cord blood	blood
6	chr3:119385400-119394400	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr3:119385600-119394200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:119385600-119394200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:119385600-119394200	Strong transcription	Fetal Thymus	thymus
10	chr3:119385600-119394400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:119385600-119394600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:119386000-119394200	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:119386000-119394200	Strong transcription	Placenta	Placenta
14	chr3:119386200-119394200	Strong transcription	Dnd41	blood
15	chr3:119386400-119394200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr3:119386400-119394400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr3:119386600-119394200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:119387000-119394200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:119387400-119394200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:119387400-119394400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:119387400-119394600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:119387400-119394600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:119387400-119394600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr3:119387800-119394600	Weak transcription	Small Intestine	intestine
25	chr3:119388600-119394200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr3:119389000-119394200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:119389000-119394400	Weak transcription	Hela-S3	cervix
28	chr3:119389000-119394400	Strong transcription	HSMM	muscle
29	chr3:119389200-119394400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:119389200-119394600	Weak transcription	Right Atrium	heart
31	chr3:119389200-119394600	Weak transcription	NHDF-Ad	bronchial
32	chr3:119389400-119394200	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:119389400-119394200	Strong transcription	A549	lung
34	chr3:119390000-119394200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:119390200-119394200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:119390400-119394400	Strong transcription	Brain Cingulate Gyrus	brain
37	chr3:119390600-119394200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:119390800-119394400	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:119391200-119394400	Weak transcription	Fetal Brain Male	brain
40	chr3:119391400-119394600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:119391400-119394600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr3:119392000-119394400	Strong transcription	NHEK	skin
43	chr3:119392000-119394600	Weak transcription	HUVEC	blood vessel
44	chr3:119392000-119394600	Weak transcription	K562	blood
45	chr3:119392200-119394200	Strong transcription	Osteobl	bone
46	chr3:119392200-119394400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:119392200-119395400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:119392400-119394200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:119392600-119394400	Weak transcription	HMEC	breast
50	chr3:119392600-119394600	Weak transcription	Primary hematopoietic stem cells	blood

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