Variant report

Variant	rs1957022
Chromosome Location	chr14:32926953-32926954
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10130628	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs10138310	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10141958	0.95[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10141964	0.90[ASN][1000 genomes]
rs1957020	0.81[JPT][hapmap];0.90[YRI][hapmap]
rs28504132	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28594748	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3784188	0.85[CEU][hapmap]
rs3784190	0.90[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs3784192	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[ASN][1000 genomes]
rs3784194	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[ASN][1000 genomes]
rs3825751	0.94[ASN][1000 genomes]
rs6571515	0.94[ASN][1000 genomes]
rs6571516	0.94[ASN][1000 genomes]
rs6571519	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6571520	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6571521	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6571522	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6571523	0.80[EUR][1000 genomes]
rs6571524	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6571525	0.80[EUR][1000 genomes]
rs7140949	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7143943	0.80[EUR][1000 genomes]
rs7146913	0.94[ASN][1000 genomes]
rs7149947	0.82[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs7153204	0.90[ASN][1000 genomes]
rs8010075	0.88[ASN][1000 genomes]
rs8013186	0.83[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs941744	0.84[CHB][hapmap];0.87[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	esv2758352	chr14:32858480-33016442	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2759978	chr14:32858480-33016442	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1957022	SNX6	cis	parietal	SCAN
rs1957022	C14orf147	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:32920800-32930200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr14:32923800-32927200	Weak transcription	HSMM	muscle
3	chr14:32923800-32927400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr14:32923800-32927800	Weak transcription	Colon Smooth Muscle	Colon
5	chr14:32923800-32929600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr14:32923800-32929600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr14:32923800-32936400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:32924400-32928200	Enhancers	Rectal Smooth Muscle	rectum
9	chr14:32925000-32928200	Enhancers	Fetal Heart	heart
10	chr14:32926200-32927000	Enhancers	Brain Anterior Caudate	brain
11	chr14:32926200-32928200	Enhancers	Fetal Lung	lung
12	chr14:32926200-32928600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr14:32926400-32927000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr14:32926400-32927000	Enhancers	NHLF	lung
15	chr14:32926400-32927200	Enhancers	Stomach Smooth Muscle	stomach
16	chr14:32926400-32927400	Enhancers	NHDF-Ad	bronchial
17	chr14:32926400-32927600	Enhancers	Brain Substantia Nigra	brain
18	chr14:32926400-32928200	Enhancers	Osteobl	bone
19	chr14:32926400-32928600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr14:32926400-32928600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr14:32926600-32927000	Enhancers	Brain Hippocampus Middle	brain
22	chr14:32926600-32927200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr14:32926600-32927800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr14:32926800-32927000	ZNF genes & repeats	Aorta	Aorta
25	chr14:32926800-32928000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr14:32926800-32936800	Weak transcription	Brain Cingulate Gyrus	brain

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