Variant report

Variant	rs16867153
Chromosome Location	chr2:9899906-9899907
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9780247..9783706-chr2:9899815..9903353,3	K562	blood:
2	chr2:9748514..9750852-chr2:9899112..9901012,2	K562	blood:
3	chr2:9897337..9900295-chr2:9937034..9939837,3	K562	blood:
4	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	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11889675	0.85[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12329266	1.00[ASW][hapmap];0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12619723	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13393165	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs13406396	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13412895	0.85[CEU][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16867150	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16867155	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4145374	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55683574	0.82[EUR][1000 genomes]
rs55831980	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67071207	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67169917	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72779090	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72779094	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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
rs16867153	PDIA6	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9895400-9904000	Weak transcription	Hela-S3	cervix
2	chr2:9895600-9900000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:9895600-9900200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:9895600-9900800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:9896200-9901400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:9897000-9902200	Enhancers	K562	blood
7	chr2:9898400-9900200	Weak transcription	Primary T cells from cord blood	blood
8	chr2:9898400-9900200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:9898400-9900400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:9898400-9900800	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr2:9898400-9901200	Enhancers	NHEK	skin
12	chr2:9898600-9900400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:9898600-9900400	Enhancers	Brain Anterior Caudate	brain
14	chr2:9898600-9901000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:9898600-9901000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:9898600-9901600	Enhancers	Fetal Thymus	thymus
17	chr2:9898600-9901800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:9898600-9901800	Weak transcription	Fetal Brain Female	brain
19	chr2:9898600-9903200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:9898600-9903600	Weak transcription	Osteobl	bone
21	chr2:9898600-9904000	Weak transcription	NH-A	brain
22	chr2:9898600-9904400	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:9898600-9905800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:9898600-9906000	Weak transcription	Lung	lung
25	chr2:9898600-9906200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:9898600-9906400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:9898600-9906400	Weak transcription	Placenta	Placenta
28	chr2:9898600-9906800	Enhancers	Fetal Muscle Leg	muscle
29	chr2:9898800-9900200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:9898800-9901600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:9898800-9903000	Weak transcription	Fetal Intestine Small	intestine
32	chr2:9899000-9901200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:9899200-9900200	Weak transcription	HMEC	breast
34	chr2:9899200-9900400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:9899200-9900400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:9899200-9900600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:9899200-9900600	Enhancers	Psoas Muscle	Psoas
38	chr2:9899200-9901600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:9899400-9900200	Weak transcription	Pancreas	Pancrea
40	chr2:9899400-9901000	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:9899400-9909200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:9899600-9900200	Weak transcription	A549	lung
43	chr2:9899600-9900400	Weak transcription	Right Ventricle	heart
44	chr2:9899600-9901000	Weak transcription	HSMMtube	muscle
45	chr2:9899600-9901200	Weak transcription	Fetal Heart	heart
46	chr2:9899600-9901200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr2:9899600-9901200	Weak transcription	Left Ventricle	heart
48	chr2:9899600-9901200	Weak transcription	Right Atrium	heart
49	chr2:9899600-9903200	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr2:9899600-9904800	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links