Variant report

Variant	rs6851699
Chromosome Location	chr4:76395005-76395006
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10518140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs11099546	0.86[EUR][1000 genomes]
rs11722278	1.00[CEU][hapmap]
rs11727259	0.90[EUR][1000 genomes]
rs11727923	0.95[EUR][1000 genomes]
rs11729106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs11731477	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11732511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs12644911	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12648354	0.82[ASN][1000 genomes]
rs1351094	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17278571	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1904104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2126854	1.00[CEU][hapmap]
rs2306177	0.82[ASN][1000 genomes]
rs2867919	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28785287	0.94[EUR][1000 genomes]
rs2903701	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs57275697	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6836107	0.84[ASN][1000 genomes]
rs6845472	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs6845588	0.82[ASN][1000 genomes]
rs6847297	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7683530	1.00[CEU][hapmap]

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	nsv594687	chr4:76154064-76502748	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv998511	chr4:76184807-76398377	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv534570	chr4:76214619-76498362	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6851699	RCHY1	Cis_1M	lymphoblastoid	RTeQTL
rs6851699	THAP6	cis	multi-tissue	Pritchard

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76391800-76396800	Weak transcription	HSMM	muscle
2	chr4:76392000-76395400	Weak transcription	Primary T cells from cord blood	blood
3	chr4:76392000-76396200	Weak transcription	Primary B cells from cord blood	blood
4	chr4:76392000-76402400	Weak transcription	Liver	Liver
5	chr4:76392600-76434800	Weak transcription	Gastric	stomach
6	chr4:76392800-76403000	Weak transcription	Fetal Brain Female	brain
7	chr4:76394000-76406200	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:76394000-76406600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr4:76394600-76424600	Weak transcription	Right Ventricle	heart
10	chr4:76394800-76395400	Enhancers	Fetal Heart	heart
11	chr4:76395000-76395800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr4:76395000-76401200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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