Variant report

Variant	rs12030098
Chromosome Location	chr1:241748056-241748057
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:241705464..241707473-chr1:241746825..241749623,2	MCF-7	breast:
2	chr1:241746264..241748164-chr1:241770315..241772018,2	MCF-7	breast:
3	chr1:241745713..241748645-chr1:241790250..241792527,2	K562	blood:
4	chr1:241740517..241743171-chr1:241746269..241748430,2	K562	blood:
5	chr1:241745082..241748095-chr1:241752482..241756598,4	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1053221	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[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[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10926521	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10926523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139441	0.82[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12144172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3193688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3765807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7349139	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	nsv427963	chr1:241718799-241832833	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats 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	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12030098	SLC16A6	trans	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241739000-241748600	Strong transcription	Liver	Liver
2	chr1:241740200-241759600	Strong transcription	Primary B cells from peripheral blood	blood
3	chr1:241740400-241768800	Weak transcription	Spleen	Spleen
4	chr1:241742000-241751400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:241742000-241757400	Weak transcription	Primary T cells from cord blood	blood
6	chr1:241742600-241749600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:241743000-241751400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr1:241743000-241754000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:241743000-241757400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:241743200-241768600	Weak transcription	Esophagus	oesophagus
11	chr1:241746600-241779200	Weak transcription	Lung	lung
12	chr1:241746800-241749200	Weak transcription	Gastric	stomach
13	chr1:241746800-241750000	Weak transcription	Primary B cells from cord blood	blood
14	chr1:241746800-241750200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:241746800-241750200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:241746800-241750400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:241746800-241761400	Weak transcription	GM12878-XiMat	blood
18	chr1:241746800-241779600	Weak transcription	Aorta	Aorta
19	chr1:241747000-241750200	Weak transcription	Placenta	Placenta
20	chr1:241747000-241750800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:241747000-241751000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:241747000-241751000	Weak transcription	NHEK	skin
23	chr1:241747000-241753800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:241747000-241757200	Weak transcription	HUVEC	blood vessel
25	chr1:241747200-241751000	Weak transcription	HMEC	breast

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