Variant report

Variant	rs7414227
Chromosome Location	chr1:153848996-153848997
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153848173..153850836-chr1:153853449..153856009,2	MCF-7	breast:
2	chr1:153848462..153850592-chr1:153853019..153855568,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10127484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10494303	0.81[CEU][hapmap]
rs10908512	0.85[EUR][1000 genomes]
rs10908525	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908526	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908578	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs11264573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264621	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264736	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1127091	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1139620	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11800001	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12117078	1.00[JPT][hapmap]
rs12120118	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12124424	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12130611	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12133492	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12133923	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12142639	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142733	0.90[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738361	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1591902	1.00[CHB][hapmap];0.83[YRI][hapmap]
rs17364880	1.00[JPT][hapmap]
rs2252508	0.90[ASW][hapmap];0.92[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];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2790686	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.81[MEX][hapmap];0.83[YRI][hapmap]
rs2841108	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.85[MEX][hapmap];0.81[YRI][hapmap]
rs3001365	1.00[CHB][hapmap]
rs35711150	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791186	0.81[CEU][hapmap]
rs4276953	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4341393	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4370789	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4451582	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4540690	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4581307	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4596938	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4845360	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs61803655	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6427300	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6427306	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6661009	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6668066	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6677794	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6690619	0.81[AFR][1000 genomes]
rs6700115	0.82[EUR][1000 genomes]
rs72694233	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7415004	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7522030	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7549032	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7554469	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9426935	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9426938	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9427232	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9427233	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	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

Variant related diseases (count:1)

Disease	PMID	Source
Lentiform nucleus volume	22903471	GWAS catalog

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7414227	SLC27A3	cis	cerebellum	SCAN
rs7414227	PSMD4	cis	parietal	SCAN
rs7414227	GATAD2B	cis	multi-tissue	Pritchard
rs7414227	HAX1	cis	cerebellum	SCAN
rs7414227	FLG	cis	parietal	SCAN
rs7414227	DCST2	cis	cerebellum	SCAN
rs7414227	GATAD2B	cis	cerebellum	SCAN
rs7414227	THEM5	cis	parietal	SCAN
rs7414227	S100A8	cis	parietal	SCAN
rs7414227	GBA	cis	parietal	SCAN
rs7414227	CTAG2	trans	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153800800-153850800	Weak transcription	A549	lung
2	chr1:153800800-153852800	Weak transcription	Fetal Brain Female	brain
3	chr1:153800800-153852800	Weak transcription	Placenta	Placenta
4	chr1:153800800-153852800	Weak transcription	Left Ventricle	heart
5	chr1:153800800-153853000	Weak transcription	Fetal Kidney	kidney
6	chr1:153814800-153853400	Weak transcription	HSMMtube	muscle
7	chr1:153822800-153853400	Weak transcription	HMEC	breast
8	chr1:153822800-153854200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:153825800-153852400	Weak transcription	Fetal Lung	lung
10	chr1:153825800-153853000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:153825800-153853000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:153825800-153853200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:153825800-153853200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:153825800-153887200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:153826000-153853200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:153826000-153853400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:153826200-153852800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:153826200-153853200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:153828800-153852800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:153830200-153863600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:153831800-153853000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:153833400-153854400	Weak transcription	Gastric	stomach
23	chr1:153833600-153853600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:153836800-153849000	Weak transcription	HepG2	liver
25	chr1:153837000-153893000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:153837200-153853400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:153839200-153852200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:153839200-153853000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:153839200-153853000	Weak transcription	Adipose Nuclei	Adipose
30	chr1:153839200-153853000	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:153839200-153853000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:153839200-153853400	Weak transcription	NHDF-Ad	bronchial
33	chr1:153839800-153853000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:153839800-153853400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:153839800-153853400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:153840000-153853400	Weak transcription	Liver	Liver
37	chr1:153842000-153850400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:153842200-153852000	Weak transcription	Brain Germinal Matrix	brain
39	chr1:153842200-153853600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:153842400-153849400	Weak transcription	Psoas Muscle	Psoas
41	chr1:153842400-153852800	Weak transcription	Primary B cells from peripheral blood	blood
42	chr1:153842400-153853000	Weak transcription	GM12878-XiMat	blood
43	chr1:153842400-153859400	Weak transcription	Hela-S3	cervix
44	chr1:153842600-153853200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:153842600-153853200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:153842600-153862400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:153842800-153852800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr1:153842800-153853000	Weak transcription	Fetal Intestine Large	intestine
49	chr1:153842800-153853400	Weak transcription	HSMM	muscle
50	chr1:153842800-153862800	Weak transcription	Thymus	Thymus

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