Variant report

Variant	rs11264573
Chromosome Location	chr1:153876975-153876976
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	chr1:153876373..153878542-chr1:153895885..153898675,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10127484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494303	0.81[CEU][hapmap]
rs10908512	0.86[EUR][1000 genomes]
rs10908525	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908526	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908578	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs11264621	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264736	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11800001	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12117078	1.00[JPT][hapmap]
rs12120118	0.83[EUR][1000 genomes]
rs12124424	0.82[EUR][1000 genomes]
rs12130611	0.83[EUR][1000 genomes]
rs12133492	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12142639	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12142733	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1591902	1.00[CHB][hapmap]
rs17364880	1.00[JPT][hapmap]
rs2252508	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790686	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.81[MEX][hapmap]
rs2841108	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap]
rs3001365	1.00[CHB][hapmap]
rs35711150	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3791186	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs4276953	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4370789	0.83[EUR][1000 genomes]
rs4540690	0.85[EUR][1000 genomes]
rs4581307	0.83[EUR][1000 genomes]
rs4845360	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs4845586	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6427300	0.83[EUR][1000 genomes]
rs6427306	0.82[EUR][1000 genomes]
rs6661009	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6671362	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72694233	0.83[EUR][1000 genomes]
rs7414227	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]
rs7415004	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7522030	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7549032	0.88[EUR][1000 genomes]
rs7554469	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11264573	HAX1	cis	cerebellum	SCAN
rs11264573	GATAD2B	cis	cerebellum	SCAN
rs11264573	DCST2	cis	cerebellum	SCAN
rs11264573	PSMD4	cis	parietal	SCAN
rs11264573	SLC27A3	cis	cerebellum	SCAN
rs11264573	GBA	cis	parietal	SCAN
rs11264573	CTAG2	trans	parietal	SCAN
rs11264573	FLG	cis	parietal	SCAN
rs11264573	S100A8	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153825800-153887200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:153837000-153893000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:153846200-153894200	Weak transcription	Esophagus	oesophagus
4	chr1:153853800-153892200	Weak transcription	Pancreas	Pancrea
5	chr1:153853800-153893400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:153854000-153892600	Weak transcription	Colonic Mucosa	Colon
7	chr1:153854400-153892400	Weak transcription	Aorta	Aorta
8	chr1:153854600-153892200	Weak transcription	HSMM	muscle
9	chr1:153855000-153886800	Weak transcription	Gastric	stomach
10	chr1:153855000-153886800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:153855000-153887200	Weak transcription	Ovary	ovary
12	chr1:153855000-153891800	Weak transcription	NHEK	skin
13	chr1:153855000-153892400	Weak transcription	NHLF	lung
14	chr1:153855000-153892800	Weak transcription	NH-A	brain
15	chr1:153855200-153880600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:153855400-153879600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:153855400-153892000	Weak transcription	HMEC	breast
18	chr1:153855600-153892200	Weak transcription	Fetal Kidney	kidney
19	chr1:153856000-153890400	Weak transcription	Brain Angular Gyrus	brain
20	chr1:153856000-153891600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:153860000-153890400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:153860200-153879400	Weak transcription	A549	lung
23	chr1:153861200-153891600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:153861200-153892400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:153861400-153877000	Weak transcription	NHDF-Ad	bronchial
26	chr1:153861400-153890800	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:153861600-153877200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:153861600-153879400	Weak transcription	Fetal Lung	lung
29	chr1:153862000-153884400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:153862200-153878800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:153862200-153878800	Weak transcription	K562	blood
32	chr1:153862400-153877800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:153862600-153892000	Weak transcription	Small Intestine	intestine
34	chr1:153866200-153880600	Weak transcription	Fetal Muscle Leg	muscle
35	chr1:153866400-153894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:153866600-153891600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:153866800-153887000	Weak transcription	Left Ventricle	heart
38	chr1:153866800-153892200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:153866800-153892200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:153869600-153884600	Weak transcription	HepG2	liver
41	chr1:153869600-153888200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:153870000-153892400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:153870200-153890400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:153870400-153881600	Strong transcription	Fetal Intestine Small	intestine
45	chr1:153870600-153888000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:153870800-153892400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:153871200-153877200	Weak transcription	Psoas Muscle	Psoas
48	chr1:153871400-153885800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:153871800-153879400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:153871800-153890600	Weak transcription	Brain Germinal Matrix	brain

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