Variant report

Variant	rs7529055
Chromosome Location	chr1:228636824-228636825
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228594178..228596096-chr1:228634719..228637473,2	MCF-7	breast:
2	chr1:228635196..228636992-chr1:228643144..228645156,2	MCF-7	breast:
3	chr1:228635449..228637961-chr12:122750153..122751748,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231563	Chromatin interaction
ENSG00000154370	Chromatin interaction
ENSG00000256861	Chromatin interaction
ENSG00000139719	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1007686	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10916313	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10916314	0.87[CEU][hapmap];0.93[EUR][1000 genomes]
rs10916317	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[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150918	0.84[GIH][hapmap];1.00[YRI][hapmap]
rs11581974	0.84[GIH][hapmap]
rs11587839	0.98[EUR][1000 genomes]
rs1188473	0.84[GIH][hapmap];1.00[YRI][hapmap]
rs1188482	0.89[GIH][hapmap]
rs1188483	0.89[GIH][hapmap]
rs1188487	0.89[GIH][hapmap]
rs12094956	0.84[GIH][hapmap];1.00[YRI][hapmap]
rs12131962	0.93[EUR][1000 genomes]
rs12542	0.85[CEU][hapmap]
rs12691493	0.84[GIH][hapmap];1.00[YRI][hapmap]
rs12725863	1.00[EUR][1000 genomes]
rs12735877	1.00[YRI][hapmap]
rs13373984	0.84[GIH][hapmap];1.00[YRI][hapmap]
rs1886774	0.92[EUR][1000 genomes]
rs1925714	0.85[CEU][hapmap]
rs1925730	0.85[CEU][hapmap]
rs2147959	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2230656	0.84[GIH][hapmap]
rs4653551	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4653552	0.99[EUR][1000 genomes]
rs4653960	0.99[EUR][1000 genomes]
rs474600	0.84[GIH][hapmap]
rs503391	0.84[GIH][hapmap]
rs513467	0.84[GIH][hapmap]
rs532465	0.84[GIH][hapmap]
rs564309	0.84[GIH][hapmap]
rs6426503	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[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6659690	0.99[EUR][1000 genomes]
rs6666241	0.99[EUR][1000 genomes]
rs7524236	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7555298	0.87[CEU][hapmap];0.82[TSI][hapmap];0.93[EUR][1000 genomes]
rs7555386	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
9	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
10	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv873281	chr1:228505739-228656780	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
12	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
13	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
14	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
15	nsv945353	chr1:228634866-228638058	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7529055	DUSP5P	cis	cerebellum	SCAN
rs7529055	WDR26	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228634000-228643200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:228634200-228641600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:228634200-228643000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:228634200-228644800	Weak transcription	Gastric	stomach
5	chr1:228634400-228638000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:228634400-228641600	Weak transcription	Brain Angular Gyrus	brain
7	chr1:228634400-228644200	Weak transcription	Brain Anterior Caudate	brain
8	chr1:228634400-228644600	Weak transcription	Right Atrium	heart
9	chr1:228634400-228644600	Weak transcription	Right Ventricle	heart
10	chr1:228635000-228639800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:228635000-228640200	Weak transcription	Fetal Brain Male	brain
12	chr1:228635000-228640600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:228635000-228641400	Weak transcription	Brain Germinal Matrix	brain
14	chr1:228635000-228641600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:228635000-228642000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:228635200-228637200	Enhancers	Placenta	Placenta
17	chr1:228635200-228643000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:228635200-228644200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:228635400-228639200	Weak transcription	Fetal Intestine Small	intestine
20	chr1:228635600-228641400	Weak transcription	Fetal Brain Female	brain
21	chr1:228635800-228643000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:228636000-228638400	Enhancers	K562	blood
23	chr1:228636600-228641200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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