Variant report

Variant	rs7522030
Chromosome Location	chr1:153854036-153854037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153853262..153855003-chr1:154191971..154194003,2	MCF-7	breast:
2	chr1:153848462..153850592-chr1:153853019..153855568,2	MCF-7	breast:
3	chr1:153848173..153850836-chr1:153853449..153856009,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143569	Chromatin interaction
ENSG00000143612	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10127484	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10494303	0.81[CEU][hapmap]
rs10908512	0.87[EUR][1000 genomes]
rs10908525	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908526	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908578	0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap]
rs11264573	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]
rs11264621	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11264736	0.96[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1139620	0.83[ASN][1000 genomes]
rs11800001	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12117078	1.00[JPT][hapmap]
rs12120118	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12124424	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12130611	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12133492	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12142639	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12142733	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12738361	0.83[ASN][1000 genomes]
rs17364880	1.00[JPT][hapmap]
rs2252508	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2790686	1.00[CHD][hapmap];0.80[GIH][hapmap]
rs2841108	1.00[CHD][hapmap];0.80[GIH][hapmap]
rs35711150	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3791186	0.81[CEU][hapmap]
rs4276953	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4341393	0.83[ASN][1000 genomes]
rs4370789	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4451582	0.80[ASN][1000 genomes]
rs4540690	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4581307	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4596938	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845360	1.00[CHD][hapmap];0.93[GIH][hapmap]
rs4845586	0.80[EUR][1000 genomes]
rs61803655	0.83[ASN][1000 genomes]
rs6427300	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6427306	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6661009	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6668066	0.83[ASN][1000 genomes]
rs6671362	0.82[EUR][1000 genomes]
rs6677794	0.80[EUR][1000 genomes]
rs72694233	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7414227	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]
rs7415004	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7549032	0.86[EUR][1000 genomes]
rs7554469	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9426935	0.83[ASN][1000 genomes]
rs9426938	0.83[ASN][1000 genomes]
rs9427232	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9427233	0.80[EUR][1000 genomes];0.83[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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7522030	SLC27A3	cis	cerebellum	SCAN
rs7522030	DCST2	cis	cerebellum	SCAN
rs7522030	PSMD4	cis	parietal	SCAN
rs7522030	GATAD2B	cis	cerebellum	SCAN
rs7522030	CTAG2	trans	parietal	SCAN
rs7522030	GBA	cis	parietal	SCAN
rs7522030	HAX1	cis	cerebellum	SCAN
rs7522030	FLG	cis	parietal	SCAN
rs7522030	S100A8	cis	parietal	SCAN
rs7522030	THEM5	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153822800-153854200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:153825800-153887200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:153830200-153863600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:153833400-153854400	Weak transcription	Gastric	stomach
5	chr1:153837000-153893000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:153842400-153859400	Weak transcription	Hela-S3	cervix
7	chr1:153842600-153862400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:153842800-153862800	Weak transcription	Thymus	Thymus
9	chr1:153846200-153894200	Weak transcription	Esophagus	oesophagus
10	chr1:153846400-153854400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:153846400-153871600	Weak transcription	Lung	lung
12	chr1:153849200-153854400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:153849800-153859200	Weak transcription	Psoas Muscle	Psoas
14	chr1:153850200-153858600	Weak transcription	Dnd41	blood
15	chr1:153850800-153855000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr1:153850800-153856400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:153851200-153855400	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:153852200-153856400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr1:153852400-153856400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:153852600-153855600	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr1:153852800-153854600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:153852800-153854800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:153852800-153855000	Enhancers	Left Ventricle	heart
24	chr1:153852800-153855000	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr1:153852800-153855600	Enhancers	Primary B cells from peripheral blood	blood
26	chr1:153852800-153855600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr1:153852800-153855600	Enhancers	Stomach Mucosa	stomach
28	chr1:153852800-153856200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr1:153853000-153854200	Enhancers	Fetal Intestine Large	intestine
30	chr1:153853000-153854200	Enhancers	Fetal Intestine Small	intestine
31	chr1:153853000-153854800	Enhancers	Right Atrium	heart
32	chr1:153853000-153855000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr1:153853000-153856000	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr1:153853000-153856000	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr1:153853000-153856000	Enhancers	Fetal Heart	heart
36	chr1:153853000-153856400	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr1:153853200-153854200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:153853200-153854200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:153853200-153854200	Flanking Active TSS	Fetal Brain Male	brain
40	chr1:153853200-153854600	Active TSS	Brain Germinal Matrix	brain
41	chr1:153853200-153855000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:153853200-153855000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:153853200-153855600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr1:153853200-153856000	Enhancers	Small Intestine	intestine
45	chr1:153853400-153854200	Flanking Active TSS	Fetal Lung	lung
46	chr1:153853400-153854400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:153853400-153854400	Enhancers	Primary T cells from cord blood	blood
48	chr1:153853400-153854400	Enhancers	Aorta	Aorta
49	chr1:153853400-153854400	Enhancers	Spleen	Spleen
50	chr1:153853400-153854400	Flanking Active TSS	HSMMtube	muscle

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