Variant report

Variant	rs998986
Chromosome Location	chr6:71312247-71312248
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:71139434..71142286-chr6:71311712..71314259,2	K562	blood:

Extended variants
information (count: 136 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10485118	0.86[JPT][hapmap]
rs10485119	0.86[JPT][hapmap]
rs1075262	0.88[CEU][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap]
rs1075263	0.86[JPT][hapmap]
rs10945230	0.86[JPT][hapmap]
rs10945236	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1140297	0.93[ASN][1000 genomes]
rs11965656	0.86[JPT][hapmap]
rs1208476	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs1208477	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs12190556	0.92[CEU][hapmap];0.84[CHB][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12197942	0.86[JPT][hapmap]
rs12197963	0.86[JPT][hapmap]
rs12198920	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12203298	0.86[JPT][hapmap]
rs12205103	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12209965	0.86[JPT][hapmap]
rs12215765	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12216376	0.86[JPT][hapmap]
rs12526164	0.86[JPT][hapmap]
rs12526827	0.86[JPT][hapmap]
rs12527634	0.86[JPT][hapmap]
rs12529284	0.86[JPT][hapmap]
rs13199529	0.89[ASN][1000 genomes]
rs13206086	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs13213357	0.89[ASN][1000 genomes]
rs13437371	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13654	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1534050	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16869170	0.86[JPT][hapmap]
rs16869221	0.86[JPT][hapmap]
rs16869228	0.84[JPT][hapmap]
rs16869238	0.86[JPT][hapmap]
rs16869243	0.86[JPT][hapmap]
rs16869267	0.86[JPT][hapmap]
rs16869273	0.86[JPT][hapmap]
rs16869338	0.86[JPT][hapmap]
rs16869353	0.86[JPT][hapmap]
rs16869370	0.86[JPT][hapmap]
rs16869371	0.86[JPT][hapmap]
rs16869373	0.85[JPT][hapmap]
rs16880770	0.86[JPT][hapmap]
rs1739338	0.86[JPT][hapmap]
rs1917344	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2207423	0.86[JPT][hapmap]
rs2273210	0.86[JPT][hapmap]
rs2293297	0.86[JPT][hapmap]
rs2295200	0.86[JPT][hapmap]
rs2346889	0.86[JPT][hapmap]
rs2346890	0.86[JPT][hapmap]
rs2347427	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2639297	0.86[JPT][hapmap]
rs2691505	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2691506	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747702	0.86[JPT][hapmap]
rs2747703	0.88[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs3193656	0.84[JPT][hapmap]
rs34378057	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34873840	0.81[ASN][1000 genomes]
rs35542509	0.86[ASN][1000 genomes]
rs3736751	0.86[JPT][hapmap]
rs3763251	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3846750	0.86[JPT][hapmap]
rs3889007	0.86[JPT][hapmap]
rs4283855	0.86[JPT][hapmap]
rs4496758	0.86[JPT][hapmap]
rs6455370	0.86[JPT][hapmap]
rs6455371	0.92[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs6900840	0.84[JPT][hapmap]
rs6902797	0.82[JPT][hapmap]
rs6906572	0.86[JPT][hapmap]
rs6906592	0.86[JPT][hapmap]
rs6910903	0.86[JPT][hapmap]
rs6911812	0.85[JPT][hapmap]
rs6911983	0.86[JPT][hapmap]
rs6913548	0.85[JPT][hapmap]
rs6916974	0.86[JPT][hapmap]
rs6917368	0.86[JPT][hapmap]
rs6922680	0.86[JPT][hapmap]
rs6925112	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6925839	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6926591	0.86[JPT][hapmap]
rs6930397	0.86[JPT][hapmap]
rs6933150	0.86[JPT][hapmap]
rs6933784	0.86[JPT][hapmap]
rs6939478	0.86[JPT][hapmap]
rs6939814	0.86[JPT][hapmap]
rs6940416	0.92[JPT][hapmap]
rs6942012	0.86[JPT][hapmap]
rs7341224	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7739098	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7740873	0.86[JPT][hapmap]
rs7741265	0.86[JPT][hapmap]
rs7752409	0.86[JPT][hapmap]
rs7753355	0.86[JPT][hapmap]
rs7756652	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7757026	0.86[JPT][hapmap]
rs7759464	0.86[JPT][hapmap]
rs7765110	0.86[JPT][hapmap]
rs7766075	0.86[JPT][hapmap]
rs7767109	0.86[JPT][hapmap]
rs7769582	0.86[JPT][hapmap]
rs7775962	0.86[JPT][hapmap]
rs9283835	0.86[JPT][hapmap]
rs9294868	0.86[JPT][hapmap]
rs9294872	0.86[JPT][hapmap]
rs9294874	0.86[JPT][hapmap]
rs9294876	0.86[JPT][hapmap]
rs9446245	0.86[JPT][hapmap]
rs9446248	0.81[JPT][hapmap]
rs9446267	0.86[JPT][hapmap]
rs9446271	0.93[ASN][1000 genomes]
rs9446274	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9446275	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9455092	0.86[JPT][hapmap]
rs9455104	0.86[JPT][hapmap]
rs9455113	0.86[JPT][hapmap]
rs9455121	0.86[JPT][hapmap]
rs9455130	0.86[JPT][hapmap]
rs9455132	0.86[JPT][hapmap]
rs9455133	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs9455160	0.86[JPT][hapmap]
rs9455162	0.86[JPT][hapmap]
rs9455163	0.86[JPT][hapmap]
rs9455173	0.93[ASN][1000 genomes]
rs9455179	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9455180	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9455185	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9455186	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS 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	29 gene(s)	inside rSNPs	diseases
5	nsv886145	chr6:71119524-71317480	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv886146	chr6:71219464-71317480	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv886147	chr6:71273253-71471863	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs998986	C6orf57	cis	cerebellum	SCAN
rs998986	C6orf57	cis	Thyroid	GTEx
rs998986	C6orf57	cis	multi-tissue	Pritchard
rs998986	C6orf57	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71295400-71314000	Weak transcription	Aorta	Aorta
2	chr6:71310000-71312400	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr6:71310200-71312400	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr6:71311200-71312600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:71311600-71313800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:71312000-71319000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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