Variant report

Variant	rs6701341
Chromosome Location	chr1:153974621-153974622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr1:153974371-153974742	HepG2	liver:	n/a	chr1:153974551-153974566 chr1:153974548-153974564 chr1:153974594-153974609 chr1:153974594-153974610 chr1:153974549-153974563 chr1:153974546-153974566
2	MAFK	chr1:153974325-153974706	IMR90	lung:	n/a	chr1:153974551-153974566 chr1:153974548-153974564 chr1:153974594-153974609 chr1:153974594-153974610 chr1:153974549-153974563 chr1:153974546-153974566
3	MAFF	chr1:153974450-153974638	HepG2	liver:	n/a	n/a
4	GATA3	chr1:153973853-153974733	SK-N-SH	brain:	n/a	chr1:153974246-153974254
5	MAFK	chr1:153974483-153974661	HepG2	liver:	n/a	chr1:153974551-153974566 chr1:153974548-153974564 chr1:153974594-153974609 chr1:153974594-153974610 chr1:153974549-153974563 chr1:153974546-153974566
6	JUND	chr1:153974094-153974640	HCT-116	colon:	n/a	n/a
7	GATA3	chr1:153973824-153974680	MCF-7	breast:	n/a	chr1:153974246-153974254
8	GATA3	chr1:153973954-153974682	SK-N-SH	brain:	n/a	chr1:153974246-153974254
9	TCF12	chr1:153973925-153974660	SK-N-SH	brain:	n/a	chr1:153974045-153974053

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153970147..153972030-chr1:153974534..153976756,2	K562	blood:
2	chr1:153970115..153973067-chr1:153973614..153977850,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252669	TF binding region
ENSG00000252669	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10127983	0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs10559	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs10796986	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10908557	0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs10908558	0.82[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs10908627	1.00[ASW][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs1110165	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs11264532	0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs11264680	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs11264743	0.82[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap]
rs11264763	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11264865	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11264866	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];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11264871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes]
rs11264873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes]
rs11264875	0.91[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11264886	0.83[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap]
rs11264964	0.91[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs11264974	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11265040	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs11265049	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11265076	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11265082	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs11265099	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs11265122	0.91[ASW][hapmap]
rs11581644	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs11586701	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11589857	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs11590099	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12021641	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs12022158	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12022730	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12028398	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12032914	0.82[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs12033835	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap]
rs12041920	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12042562	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12042989	0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs12043350	0.82[ASW][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs12048137	0.83[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12049128	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12401565	0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs12403956	0.94[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs12408260	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12564669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1547766	0.81[EUR][1000 genomes]
rs1547767	0.82[EUR][1000 genomes]
rs1572788	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap]
rs3748848	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs3791187	0.82[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs4521985	0.91[ASW][hapmap]
rs4845357	0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs4845583	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs4845600	0.91[ASW][hapmap]
rs4845601	0.91[ASW][hapmap]
rs61542760	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6667928	0.91[ASW][hapmap]
rs6672856	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6678826	0.91[ASW][hapmap]
rs6679907	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6680140	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs6703545	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7521303	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7537691	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7547663	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7552737	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs8450	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs946682	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[YRI][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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6701341	SLC25A44	cis	cerebellum	SCAN
rs6701341	UBAP2L	cis	multi-tissue	Pritchard
rs6701341	SPRR2D	cis	parietal	SCAN
rs6701341	SLC39A1	cis	cerebellum	SCAN
rs6701341	GATAD2B	cis	multi-tissue	Pritchard
rs6701341	CRTC2	cis	lymphoblastoid	seeQTL
rs6701341	SLC27A3	cis	cerebellum	SCAN
rs6701341	LASS2	cis	parietal	SCAN
rs6701341	CRTC2	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153965600-153975000	Weak transcription	Fetal Brain Male	brain
2	chr1:153966800-153978400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:153967000-153983600	Weak transcription	Brain Angular Gyrus	brain
4	chr1:153967200-153976000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:153967800-153977400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:153968400-153976000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:153968400-153976400	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:153968400-153978200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:153968400-153978200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr1:153968400-153978600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:153968400-153986200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:153968400-153987000	Weak transcription	Brain Anterior Caudate	brain
13	chr1:153968400-153988400	Weak transcription	Primary B cells from cord blood	blood
14	chr1:153968800-153976200	Weak transcription	Fetal Brain Female	brain
15	chr1:153972800-153974800	Enhancers	Fetal Heart	heart
16	chr1:153972800-153975400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr1:153973000-153975400	Enhancers	Placenta	Placenta
18	chr1:153973600-153975400	Enhancers	NH-A	brain
19	chr1:153973600-153998000	Weak transcription	Brain Substantia Nigra	brain
20	chr1:153973800-153974800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:153974200-153974800	Enhancers	HMEC	breast
22	chr1:153974200-153975600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:153974400-153974800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:153974400-153976200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:153974600-153974800	Enhancers	HepG2	liver
26	chr1:153974600-153978400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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