Variant report

Variant	rs10916262
Chromosome Location	chr1:228231601-228231602
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228230109..228232010-chr1:228259554..228261382,2	MCF-7	breast:
2	chr1:228230593..228233743-chr1:228266811..228273047,6	MCF-7	breast:
3	chr1:228197532..228200122-chr1:228231400..228233499,2	MCF-7	breast:
4	chr1:228222291..228225840-chr1:228229698..228232365,4	MCF-7	breast:
5	chr1:228226578..228229200-chr1:228230155..228231993,2	MCF-7	breast:
6	chr1:228230050..228232873-chr1:228260583..228263014,2	MCF-7	breast:
7	chr1:228229732..228234338-chr1:228270201..228272073,4	MCF-7	breast:
8	chr1:228230710..228233813-chr1:228249288..228252101,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143761	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1034792	0.92[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1048503	1.00[ASW][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10495278	1.00[ASW][hapmap];0.86[CHB][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs10495279	0.80[MKK][hapmap]
rs10916261	0.92[EUR][1000 genomes]
rs11577976	1.00[ASW][hapmap]
rs11577983	0.80[ASN][1000 genomes]
rs11578623	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11579725	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11582265	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582704	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584499	1.00[ASW][hapmap];0.84[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11589007	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11589040	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11589467	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11589513	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590118	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1188977	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12033088	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12048010	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13374948	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs1620734	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1745420	0.92[EUR][1000 genomes]
rs1745422	0.98[EUR][1000 genomes]
rs17621519	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1909647	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2070960	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2107905	0.92[EUR][1000 genomes]
rs3738680	1.00[ASW][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3738681	1.00[ASW][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3768329	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768330	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820624	0.81[AMR][1000 genomes]
rs41270175	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41270177	0.98[EUR][1000 genomes]
rs4363416	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4546914	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4653533	0.91[CEU][hapmap]
rs4653894	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4653897	0.98[EUR][1000 genomes]
rs56888086	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57146523	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57657087	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60213528	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61825125	0.86[EUR][1000 genomes]
rs61825130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61825131	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61825133	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61825135	0.81[AMR][1000 genomes]
rs6672422	0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs6672559	0.87[TSI][hapmap]
rs6672601	0.83[EUR][1000 genomes]
rs72756204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72756209	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7530812	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7539664	0.92[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs822727	0.81[EUR][1000 genomes]
rs860301	0.81[EUR][1000 genomes]
rs882451	1.00[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9287011	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv945349	chr1:228186556-228245135	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	esv3436262	chr1:228228329-228232627	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv1814215	chr1:228231601-228259932	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
12	esv1844252	chr1:228231601-228259932	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
13	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
14	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10916262	MIXL1	cis	cerebellum	SCAN
rs10916262	OBSCN	cis	cerebellum	SCAN
rs10916262	LEFTY1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228230400-228232800	Weak transcription	Esophagus	oesophagus
2	chr1:228231000-228232000	Enhancers	Hela-S3	cervix
3	chr1:228231400-228232600	Weak transcription	Stomach Mucosa	stomach
4	chr1:228231400-228239600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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