Variant report

Variant	rs6856688
Chromosome Location	chr4:87243340-87243341
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11938088	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11939109	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12503051	0.86[JPT][hapmap]
rs12508801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12511114	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12511135	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12512698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12644920	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17011731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17011843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17011890	0.86[JPT][hapmap]
rs17011950	0.86[JPT][hapmap]
rs2199307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869444	0.93[JPT][hapmap]
rs2904095	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2904105	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35334656	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4235079	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4235080	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4488910	0.93[JPT][hapmap]
rs4693145	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55642851	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56054148	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56805412	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59277757	0.88[ASN][1000 genomes]
rs60079003	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61686149	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6531925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6817640	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6829684	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6843457	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6849834	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73835402	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73838707	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73838904	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73838906	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7669675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7675359	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7697335	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003585	chr4:86957967-87250436	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv934210	chr4:87197339-87325578	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1011494	chr4:87221480-87257453	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv1007891	chr4:87230601-87252524	Strong transcription Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv461574	chr4:87239764-87279096	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv594788	chr4:87239764-87279096	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6856688	HERC6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87232600-87247400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr4:87235200-87250200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:87239400-87252400	Weak transcription	Brain Angular Gyrus	brain
4	chr4:87239400-87254400	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:87239400-87258600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:87241200-87247200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:87242000-87270000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:87242800-87243800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:87243000-87243800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr4:87243000-87244600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:87243200-87243600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr4:87243200-87243600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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