Variant report

Variant	rs11626343
Chromosome Location	chr14:31673666-31673667
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	chr14:31671940..31673668-chr14:31776880..31779409,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11620816	0.96[EUR][1000 genomes]
rs11622403	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11624437	0.92[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs11625570	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11625798	0.97[EUR][1000 genomes]
rs11845860	0.96[EUR][1000 genomes]
rs11848094	0.91[EUR][1000 genomes]
rs11848563	0.96[EUR][1000 genomes]
rs12879409	0.88[JPT][hapmap]
rs17097688	0.92[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs17097735	1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs17097741	0.92[CEU][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs17097743	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34039100	0.84[EUR][1000 genomes]
rs34684806	0.97[EUR][1000 genomes]
rs34745649	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3954287	0.91[EUR][1000 genomes]
rs45610935	0.85[EUR][1000 genomes]
rs56168081	0.93[EUR][1000 genomes]
rs56346233	0.93[EUR][1000 genomes]
rs57000706	0.93[EUR][1000 genomes]
rs57893693	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58071351	0.93[EUR][1000 genomes]
rs58204331	0.94[EUR][1000 genomes]
rs58771204	0.85[EUR][1000 genomes]
rs59458716	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59933112	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60350855	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60928004	0.93[EUR][1000 genomes]
rs61592116	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66528205	0.91[EUR][1000 genomes]
rs67960414	0.93[EUR][1000 genomes]
rs72670334	0.83[EUR][1000 genomes]
rs72670351	0.93[EUR][1000 genomes]
rs72670364	0.93[EUR][1000 genomes]
rs72670371	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72670374	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72670375	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72670377	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72670385	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72670390	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72670391	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72670396	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72670398	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72670399	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9888564	1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901587	chr14:31501505-31752664	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv832763	chr14:31501597-31680021	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1050054	chr14:31501703-31733642	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	26 gene(s)	inside rSNPs	diseases
4	nsv1043033	chr14:31538984-31686696	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv2830427	chr14:31639110-32000034	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11626343	PRKD1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31637200-31675000	Weak transcription	Gastric	stomach
2	chr14:31640800-31674000	Weak transcription	Fetal Brain Male	brain
3	chr14:31643200-31675000	Weak transcription	Esophagus	oesophagus
4	chr14:31643400-31675000	Weak transcription	Spleen	Spleen
5	chr14:31644800-31675000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:31644800-31675000	Weak transcription	Pancreas	Pancrea
7	chr14:31645600-31675000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr14:31646600-31674400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr14:31648000-31674800	Weak transcription	Thymus	Thymus
10	chr14:31651000-31674800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr14:31654400-31674800	Weak transcription	Colonic Mucosa	Colon
12	chr14:31655000-31674400	Weak transcription	Fetal Brain Female	brain
13	chr14:31659800-31673800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr14:31660200-31675000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr14:31660600-31674200	Weak transcription	Brain Germinal Matrix	brain
16	chr14:31660800-31675000	Weak transcription	Fetal Thymus	thymus
17	chr14:31664200-31673800	Genic enhancers	HepG2	liver
18	chr14:31664400-31674800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr14:31664400-31675000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr14:31664600-31673800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr14:31664600-31674000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr14:31665200-31673800	Weak transcription	HMEC	breast
23	chr14:31665200-31675000	Weak transcription	Small Intestine	intestine
24	chr14:31665400-31674200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr14:31665400-31674200	Weak transcription	Fetal Heart	heart
26	chr14:31665400-31674800	Weak transcription	Aorta	Aorta
27	chr14:31665400-31675000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr14:31665600-31674000	Weak transcription	NHLF	lung
29	chr14:31665600-31674800	Weak transcription	HSMMtube	muscle
30	chr14:31666400-31675000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr14:31666600-31674800	Weak transcription	Right Ventricle	heart
32	chr14:31666800-31674800	Weak transcription	Ovary	ovary
33	chr14:31667200-31674000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr14:31667200-31674200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr14:31667200-31674400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr14:31667200-31674400	Weak transcription	Stomach Mucosa	stomach
37	chr14:31667200-31674400	Weak transcription	Hela-S3	cervix
38	chr14:31667400-31674200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr14:31667800-31674200	Weak transcription	Colon Smooth Muscle	Colon
40	chr14:31668200-31674000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr14:31669000-31673800	Strong transcription	Primary T cells from cord blood	blood
42	chr14:31669000-31673800	Strong transcription	Fetal Lung	lung
43	chr14:31669400-31674000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr14:31669400-31674200	Weak transcription	Brain Substantia Nigra	brain
45	chr14:31669400-31675000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr14:31669600-31674000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr14:31669600-31674000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr14:31669600-31674000	Weak transcription	Osteobl	bone
49	chr14:31669600-31674200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr14:31669600-31674200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links