Variant report

Variant	rs2332835
Chromosome Location	chr14:72919636-72919637
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10131300	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.89[YRI][hapmap];0.90[ASN][1000 genomes]
rs10151157	0.95[CEU][hapmap]
rs11158958	1.00[CHB][hapmap]
rs1155166	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1157500	1.00[CHB][hapmap]
rs11628490	0.96[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs12433564	0.81[CEU][hapmap];0.96[YRI][hapmap];0.90[ASN][1000 genomes]
rs12436059	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860152	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2159194	0.81[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2238189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286069	1.00[CHB][hapmap]
rs4903015	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4903019	0.86[EUR][1000 genomes]
rs4903020	0.96[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs4903022	0.87[EUR][1000 genomes]
rs4903025	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4903026	0.81[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4903029	1.00[CHB][hapmap]
rs6574077	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7143134	0.96[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs7143154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7143912	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7146819	0.86[EUR][1000 genomes]
rs7153455	0.92[CEU][hapmap];1.00[CHD][hapmap]
rs7155105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7158962	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7159439	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs7160019	1.00[CHB][hapmap]
rs719064	0.96[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs758265	0.81[CEU][hapmap]
rs8012037	0.94[ASW][hapmap];0.81[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs8013020	1.00[CHB][hapmap]
rs8018108	0.96[CEU][hapmap];1.00[CHD][hapmap]
rs9989171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];1.00[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	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv948800	chr14:72462557-73150701	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2332835	VSX2	cis	parietal	SCAN
rs2332835	DCAF5	cis	parietal	SCAN
rs2332835	ZNF410	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72913800-72922600	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr14:72916200-72920000	Enhancers	Fetal Stomach	stomach
3	chr14:72916400-72919800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr14:72917200-72919800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr14:72917200-72919800	Enhancers	Fetal Kidney	kidney
6	chr14:72917200-72919800	Enhancers	Fetal Muscle Leg	muscle
7	chr14:72917400-72919800	Enhancers	Fetal Thymus	thymus
8	chr14:72917400-72921000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr14:72917600-72919800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr14:72917600-72919800	Enhancers	Fetal Muscle Trunk	muscle
11	chr14:72917600-72919800	Enhancers	HSMMtube	muscle
12	chr14:72917600-72921400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr14:72917800-72920000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr14:72918000-72924400	Weak transcription	Spleen	Spleen
15	chr14:72918000-72930000	Weak transcription	Right Atrium	heart
16	chr14:72918200-72920000	Enhancers	Dnd41	blood
17	chr14:72918200-72929000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr14:72918200-72930000	Weak transcription	Left Ventricle	heart
19	chr14:72918400-72919800	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr14:72918400-72924200	Weak transcription	HSMM	muscle
21	chr14:72918600-72919800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr14:72918600-72919800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr14:72918800-72919800	Enhancers	Primary T cells from cord blood	blood
24	chr14:72918800-72919800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr14:72918800-72919800	Enhancers	Esophagus	oesophagus
26	chr14:72918800-72924200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr14:72919000-72919800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr14:72919000-72920000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
29	chr14:72919000-72920200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr14:72919000-72924200	Weak transcription	NH-A	brain
31	chr14:72919000-72931400	Weak transcription	Adipose Nuclei	Adipose
32	chr14:72919400-72919800	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr14:72919400-72921200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr14:72919400-72926800	Weak transcription	Fetal Intestine Small	intestine
35	chr14:72919400-72945200	Weak transcription	Brain Germinal Matrix	brain
36	chr14:72919600-72920000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr14:72919600-72920000	Enhancers	GM12878-XiMat	blood

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