Variant report

Variant	rs12619723
Chromosome Location	chr2:9899479-9899480
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9899081..9899639-chr3:43902591..43903091,2	MCF-7	breast:
2	chr2:9897830..9899713-chr2:9900837..9903744,2	K562	blood:
3	chr2:9748514..9750852-chr2:9899112..9901012,2	K562	blood:
4	chr2:9897337..9900295-chr2:9937034..9939837,3	K562	blood:
5	chr2:9893059..9895633-chr2:9899321..9902671,3	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10189991	0.92[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11889675	0.92[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12329266	0.94[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13393165	0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs13406396	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13412895	0.92[CEU][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16867150	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16867153	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16867155	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4145374	0.92[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55683574	0.81[EUR][1000 genomes]
rs55831980	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67071207	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67169917	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72779090	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72779094	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1014911	chr2:9863969-9905959	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv873618	chr2:9870631-9919759	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv873619	chr2:9870631-9956981	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv518227	chr2:9893454-9909114	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12619723	PDIA6	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9894600-9899800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:9894800-9899600	Enhancers	Esophagus	oesophagus
3	chr2:9895400-9904000	Weak transcription	Hela-S3	cervix
4	chr2:9895600-9900000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:9895600-9900200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:9895600-9900800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:9896200-9901400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:9896800-9899600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr2:9896800-9899800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr2:9897000-9902200	Enhancers	K562	blood
11	chr2:9898200-9899600	Enhancers	Right Ventricle	heart
12	chr2:9898400-9899600	Enhancers	Fetal Lung	lung
13	chr2:9898400-9899600	Enhancers	Right Atrium	heart
14	chr2:9898400-9899800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:9898400-9899800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:9898400-9900200	Weak transcription	Primary T cells from cord blood	blood
17	chr2:9898400-9900200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:9898400-9900400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:9898400-9900800	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr2:9898400-9901200	Enhancers	NHEK	skin
21	chr2:9898600-9899600	Enhancers	Fetal Muscle Trunk	muscle
22	chr2:9898600-9899600	Enhancers	HSMMtube	muscle
23	chr2:9898600-9899800	Weak transcription	Thymus	Thymus
24	chr2:9898600-9900400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:9898600-9900400	Enhancers	Brain Anterior Caudate	brain
26	chr2:9898600-9901000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:9898600-9901000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:9898600-9901600	Enhancers	Fetal Thymus	thymus
29	chr2:9898600-9901800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:9898600-9901800	Weak transcription	Fetal Brain Female	brain
31	chr2:9898600-9903200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:9898600-9903600	Weak transcription	Osteobl	bone
33	chr2:9898600-9904000	Weak transcription	NH-A	brain
34	chr2:9898600-9904400	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:9898600-9905800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:9898600-9906000	Weak transcription	Lung	lung
37	chr2:9898600-9906200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:9898600-9906400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:9898600-9906400	Weak transcription	Placenta	Placenta
40	chr2:9898600-9906800	Enhancers	Fetal Muscle Leg	muscle
41	chr2:9898800-9899600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:9898800-9899600	Enhancers	A549	lung
43	chr2:9898800-9900200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:9898800-9901600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:9898800-9903000	Weak transcription	Fetal Intestine Small	intestine
46	chr2:9899000-9899600	Enhancers	Fetal Heart	heart
47	chr2:9899000-9901200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:9899200-9900200	Weak transcription	HMEC	breast
49	chr2:9899200-9900400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr2:9899200-9900400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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