Variant report

Variant	rs6677660
Chromosome Location	chr1:174014507-174014508
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	chr1:174012544..174014524-chr1:174017361..174019200,2	K562	blood:
2	chr1:173990725..173993170-chr1:174013913..174015825,2	K562	blood:

Variant related genes	Relation type
ENSG00000135870	Chromatin interaction
ENSG00000224977	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10798301	0.87[CHB][hapmap]
rs10798302	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10912719	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912722	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12058585	0.87[ASW][hapmap];0.89[MEX][hapmap]
rs12063313	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12066153	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12071784	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs12076799	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12079062	0.83[CHB][hapmap]
rs12089405	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs12092774	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12096785	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12097809	0.89[ASN][1000 genomes]
rs12563301	0.87[CHB][hapmap]
rs12563395	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12566651	0.87[ASW][hapmap];0.91[MEX][hapmap]
rs12568409	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1322775	0.87[CHB][hapmap]
rs1322777	0.87[CHB][hapmap]
rs1322780	0.87[CHB][hapmap]
rs13375086	0.88[ASN][1000 genomes]
rs13376011	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1417186	0.90[YRI][hapmap]
rs16846683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17350956	1.00[YRI][hapmap]
rs17350991	0.89[YRI][hapmap]
rs17353198	0.90[YRI][hapmap]
rs1799876	0.91[CHB][hapmap]
rs1884994	0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs1951627	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs2860841	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs3980286	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs4592301	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4650945	0.83[CHB][hapmap]
rs4650968	0.90[YRI][hapmap]
rs4652169	0.87[CHB][hapmap]
rs4652179	0.90[YRI][hapmap]
rs4652283	0.85[CEU][hapmap]
rs4652298	0.85[CEU][hapmap]
rs4652328	0.85[CEU][hapmap]
rs56247945	0.88[ASN][1000 genomes]
rs5878	0.87[CHB][hapmap]
rs61547493	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826843	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61826844	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61827891	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61827894	0.83[EUR][1000 genomes]
rs6425262	0.92[MEX][hapmap]
rs6425267	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs6425273	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6425275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6661182	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs6661868	0.84[ASN][1000 genomes]
rs6663875	0.87[CHB][hapmap]
rs6665484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6665880	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs6668008	0.90[YRI][hapmap]
rs6673632	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6678487	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6686083	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6689285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6695327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6695887	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs6696076	0.83[CHB][hapmap]
rs6696163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6699146	0.87[CHB][hapmap]
rs6703547	0.84[MEX][hapmap]
rs714624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7413166	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7511780	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7514069	0.82[ASN][1000 genomes]
rs7528380	0.84[MEX][hapmap]
rs7533430	0.83[CHB][hapmap]
rs7538312	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7547280	0.88[ASN][1000 genomes]
rs7547880	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs7553788	0.86[CHB][hapmap]
rs7554915	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs767053	0.87[ASW][hapmap];0.91[MEX][hapmap]
rs9286895	0.87[CHB][hapmap]
rs941989	0.87[CHB][hapmap]
rs9425430	0.87[CHB][hapmap]
rs9425431	0.85[CEU][hapmap]
rs9425433	0.85[CEU][hapmap]
rs9425766	0.87[CHB][hapmap]
rs9661233	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv872551	chr1:173913804-174025660	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	nsv465661	chr1:174014507-174152688	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv548193	chr1:174014507-174152688	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6677660	PRDX6	cis	parietal	SCAN
rs6677660	SLC9A11	cis	parietal	SCAN
rs6677660	RABGAP1L	cis	parietal	SCAN
rs6677660	SERPINC1	cis	Esophagus Mucosa	GTEx
rs6677660	C1orf156	cis	parietal	SCAN
rs6677660	SNORD78	cis	parietal	SCAN
rs6677660	CENPL	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174010200-174020800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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