Variant report

Variant	rs11628490
Chromosome Location	chr14:72912961-72912962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1004477	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs10139793	0.82[ASN][1000 genomes]
rs10151157	0.91[CEU][hapmap]
rs1155166	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs12436059	0.91[EUR][1000 genomes]
rs12436819	0.90[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs17115530	0.92[JPT][hapmap]
rs17115702	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs17115708	0.90[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs1860152	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2238189	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2238190	0.80[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2239211	0.90[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs2332835	0.96[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4903015	0.88[CEU][hapmap]
rs4903019	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4903020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4903022	0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4903025	0.86[EUR][1000 genomes]
rs4903027	0.81[CHD][hapmap]
rs58470149	0.90[ASN][1000 genomes]
rs7143134	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7143154	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs7143912	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7146819	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7153455	0.88[CEU][hapmap]
rs7155105	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs7158962	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs719064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs740536	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs8018108	0.92[CEU][hapmap]
rs8022670	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9989171	0.96[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][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
rs11628490	C14orf162	cis	cerebellum	SCAN
rs11628490	ZNF410	cis	parietal	SCAN
rs11628490	VSX2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72906600-72913600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr14:72908400-72917600	Weak transcription	Lung	lung
3	chr14:72911600-72916200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr14:72911600-72916400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr14:72911600-72916400	Weak transcription	Dnd41	blood
6	chr14:72911800-72913800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr14:72911800-72916200	Weak transcription	GM12878-XiMat	blood
8	chr14:72911800-72917200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr14:72911800-72917200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr14:72911800-72917600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr14:72912000-72916400	Weak transcription	Primary T cells from cord blood	blood
12	chr14:72912000-72917000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr14:72912000-72917200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr14:72912000-72917400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr14:72912200-72917400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr14:72912400-72913600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr14:72912600-72914000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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