Variant report

Variant	rs2299920
Chromosome Location	chr14:78051271-78051272
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78050054..78053077-chr14:78055760..78058382,3	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10135955	0.85[CHB][hapmap]
rs10149237	0.99[ASN][1000 genomes]
rs10151331	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10151712	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10400797	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873307	0.99[ASN][1000 genomes]
rs10873309	0.81[CHD][hapmap]
rs11159280	0.99[ASN][1000 genomes]
rs12147112	0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[ASN][1000 genomes]
rs12148048	0.98[ASN][1000 genomes]
rs12588462	0.94[CHB][hapmap]
rs12589986	0.82[ASN][1000 genomes]
rs12884431	0.80[ASN][1000 genomes]
rs12885003	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106022	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1997561	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs1997562	0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[ASN][1000 genomes]
rs2267750	0.81[CHD][hapmap]
rs2299917	0.83[ASN][1000 genomes]
rs2299919	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2299921	0.81[CHD][hapmap]
rs2299924	0.83[CHD][hapmap]
rs8018813	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832835	chr14:77906706-78095207	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active 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 miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2299920	PAPLN	cis	cerebellum	SCAN
rs2299920	COQ6	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77987800-78060000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr14:78013200-78066200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr14:78016400-78061000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr14:78021800-78061000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr14:78021800-78068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:78021800-78071600	Weak transcription	Colon Smooth Muscle	Colon
7	chr14:78022000-78060800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr14:78022400-78055000	Weak transcription	Colonic Mucosa	Colon
9	chr14:78030200-78056800	Weak transcription	HMEC	breast
10	chr14:78040400-78051800	Weak transcription	HepG2	liver
11	chr14:78042400-78059000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:78042400-78060800	Weak transcription	Aorta	Aorta
13	chr14:78042400-78066600	Weak transcription	Fetal Brain Female	brain
14	chr14:78042600-78061800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr14:78043000-78059800	Weak transcription	A549	lung
16	chr14:78043200-78058800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr14:78043800-78052200	Weak transcription	Primary B cells from cord blood	blood
18	chr14:78043800-78060800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr14:78043800-78061000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr14:78043800-78061200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr14:78043800-78061800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr14:78044000-78060600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr14:78044000-78061000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr14:78044000-78061200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr14:78044400-78054600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr14:78044600-78053600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr14:78044600-78061000	Weak transcription	Thymus	Thymus
28	chr14:78047200-78055000	Weak transcription	Fetal Thymus	thymus
29	chr14:78047400-78070000	Weak transcription	Fetal Brain Male	brain
30	chr14:78047600-78054400	Weak transcription	Stomach Mucosa	stomach
31	chr14:78047600-78055400	Weak transcription	Dnd41	blood
32	chr14:78047600-78059600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr14:78047800-78052200	Enhancers	HUVEC	blood vessel
34	chr14:78047800-78052800	Weak transcription	Fetal Heart	heart
35	chr14:78047800-78054800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr14:78047800-78059800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr14:78047800-78061000	Weak transcription	Brain Germinal Matrix	brain
38	chr14:78048000-78056600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr14:78048000-78059800	Weak transcription	K562	blood
40	chr14:78048000-78061400	Weak transcription	Fetal Intestine Small	intestine
41	chr14:78048200-78052600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr14:78048200-78052800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr14:78048200-78054400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr14:78048200-78054400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr14:78048200-78054400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr14:78048200-78056400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr14:78048200-78056400	Weak transcription	NHEK	skin
48	chr14:78048200-78056600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr14:78048200-78057200	Weak transcription	Fetal Intestine Large	intestine
50	chr14:78048200-78059600	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links