Variant report

Variant	rs6804201
Chromosome Location	chr3:23577636-23577637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23576275..23577975-chr3:23583689..23585549,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11926646	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12486880	0.88[ASN][1000 genomes]
rs12637722	0.87[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1463836	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17013412	0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17013457	0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1874913	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2133330	0.81[ASW][hapmap];0.85[CEU][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs34710747	0.89[EUR][1000 genomes]
rs35169377	0.90[ASN][1000 genomes]
rs4399836	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4642064	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs55732421	0.86[AFR][1000 genomes]
rs55779138	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56132801	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56667039	0.90[ASN][1000 genomes]
rs56964757	0.80[AFR][1000 genomes]
rs57258152	0.88[EUR][1000 genomes]
rs57278918	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs57604595	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs57801020	0.84[EUR][1000 genomes]
rs57989144	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs58068931	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs58486254	0.88[EUR][1000 genomes]
rs61363919	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6550765	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs66900833	0.88[ASN][1000 genomes]
rs6775891	0.91[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6775907	1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.95[ASN][1000 genomes]
rs6781388	0.81[AFR][1000 genomes]
rs6782079	1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6799234	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6800822	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6801946	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6802488	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs73043636	0.88[EUR][1000 genomes]
rs73043687	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs73045615	0.91[AFR][1000 genomes]
rs73045617	0.81[AFR][1000 genomes]
rs73045660	0.87[AFR][1000 genomes]
rs73049414	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7609845	0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7610906	0.88[GIH][hapmap]
rs7620266	0.88[EUR][1000 genomes]
rs7624174	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7628135	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7628949	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7631705	0.86[YRI][hapmap]
rs7632814	0.84[CEU][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7640458	0.85[CEU][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs7643270	0.88[EUR][1000 genomes]
rs9812300	0.85[CEU][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs9835324	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9854488	0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9873979	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6804201	SLC4A7	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23550800-23598600	Weak transcription	HSMMtube	muscle
2	chr3:23553000-23589600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:23567400-23589800	Weak transcription	Psoas Muscle	Psoas
4	chr3:23569400-23578600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:23570400-23578200	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:23570600-23584400	Weak transcription	Primary T cells from cord blood	blood
7	chr3:23571200-23591600	Weak transcription	GM12878-XiMat	blood
8	chr3:23571400-23598800	Weak transcription	Adipose Nuclei	Adipose
9	chr3:23572400-23578600	Weak transcription	Brain Substantia Nigra	brain
10	chr3:23572800-23579400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:23573800-23578800	Strong transcription	Primary B cells from cord blood	blood
12	chr3:23574800-23578000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:23574800-23578600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:23574800-23579800	Weak transcription	Aorta	Aorta
15	chr3:23575600-23578800	Weak transcription	Fetal Lung	lung
16	chr3:23576000-23578600	Weak transcription	Brain Anterior Caudate	brain
17	chr3:23576400-23578400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:23577000-23578200	Weak transcription	Fetal Heart	heart
19	chr3:23577400-23578600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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