Variant report

Variant	rs41227
Chromosome Location	chr14:71826787-71826788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:71802119..71805071-chr14:71825768..71827971,2	K562	blood:
2	chr14:71826599..71830607-chr14:71841838..71843609,3	K562	blood:
3	chr14:71826599..71830201-chr14:71841493..71843609,3	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10130652	0.81[EUR][1000 genomes]
rs11628525	0.80[MEX][hapmap]
rs12878009	0.84[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12897119	0.84[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs193440	0.88[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs193441	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193442	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193443	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2041330	0.81[CEU][hapmap]
rs3088206	0.81[EUR][1000 genomes]
rs36535	0.86[AMR][1000 genomes]
rs41217	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41218	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41219	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41220	0.83[ASW][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes]
rs41224	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41225	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41229	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4464023	0.84[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap]
rs7141155	0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap]
rs7153726	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7154208	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8007271	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8007521	0.84[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8016217	0.84[CEU][hapmap];0.81[CHB][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs8023058	0.88[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs917391	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832827	chr14:71676178-71833519	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv1831401	chr14:71786411-71845264	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs41227	VSX2	cis	parietal	SCAN
rs41227	SLC8A3	cis	cerebellum	SCAN
rs41227	SIPA1L1	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71805400-71828600	Weak transcription	Dnd41	blood
2	chr14:71806600-71838400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr14:71808400-71829800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr14:71808800-71838600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr14:71812200-71838800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr14:71813400-71829000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr14:71816200-71827800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr14:71816600-71826800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr14:71820000-71833600	Enhancers	Primary B cells from peripheral blood	blood
10	chr14:71820200-71838600	Weak transcription	Hela-S3	cervix
11	chr14:71820600-71838800	Weak transcription	Primary T cells from cord blood	blood
12	chr14:71821800-71828600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:71822000-71828400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr14:71822400-71829600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr14:71822600-71828400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr14:71822800-71827200	Enhancers	Primary B cells from cord blood	blood
17	chr14:71822800-71828000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr14:71822800-71828000	Weak transcription	NH-A	brain
19	chr14:71822800-71828200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr14:71822800-71828200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr14:71822800-71828800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr14:71822800-71830000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr14:71822800-71830000	Weak transcription	HSMM	muscle
24	chr14:71822800-71830800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr14:71823000-71826800	Enhancers	Rectal Smooth Muscle	rectum
26	chr14:71823000-71827800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr14:71823000-71827800	Weak transcription	Osteobl	bone
28	chr14:71823000-71828000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr14:71823000-71828200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr14:71823000-71828200	Weak transcription	Esophagus	oesophagus
31	chr14:71823000-71828600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr14:71823000-71828600	Weak transcription	Fetal Brain Female	brain
33	chr14:71823000-71829000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr14:71823000-71829600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr14:71823000-71829600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr14:71823000-71829800	Weak transcription	Brain Anterior Caudate	brain
37	chr14:71823000-71829800	Weak transcription	Brain Hippocampus Middle	brain
38	chr14:71823000-71829800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr14:71823000-71829800	Weak transcription	Fetal Brain Male	brain
40	chr14:71823000-71830000	Weak transcription	Brain Angular Gyrus	brain
41	chr14:71823000-71830600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr14:71823000-71831800	Weak transcription	Lung	lung
43	chr14:71823200-71829800	Weak transcription	Fetal Stomach	stomach
44	chr14:71823400-71827000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr14:71823400-71828200	Weak transcription	Adipose Nuclei	Adipose
46	chr14:71823400-71830400	Weak transcription	Fetal Muscle Leg	muscle
47	chr14:71823400-71830400	Weak transcription	Ovary	ovary
48	chr14:71823800-71829200	ZNF genes & repeats	GM12878-XiMat	blood
49	chr14:71824000-71827800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr14:71824200-71827800	Weak transcription	HMEC	breast

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