Variant report

Variant	rs7162579
Chromosome Location	chr15:99663230-99663231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:99649749..99652063-chr15:99662679..99664537,2	MCF-7	breast:
2	chr15:99652267..99657709-chr15:99661798..99664247,5	MCF-7	breast:
3	chr15:99658366..99661719-chr15:99663030..99668142,6	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12324825	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12591477	0.81[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs12595385	0.81[CHB][hapmap]
rs12911794	0.89[ASN][1000 genomes]
rs12915572	0.83[ASN][1000 genomes]
rs1530920	0.81[MEX][hapmap]
rs1670237	0.85[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1810091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1965866	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1965867	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305446	0.83[AMR][1000 genomes]
rs34567778	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34878632	0.82[EUR][1000 genomes]
rs55905808	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56009713	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7164548	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs8026991	0.82[CHB][hapmap]
rs8029732	1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8032817	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8037159	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8038392	0.85[CHB][hapmap]
rs8038845	0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8041213	0.91[ASN][1000 genomes]
rs896700	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs906760	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv533375	chr15:99443534-99696221	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
16	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7162579	LYSMD4	cis	cerebellum	SCAN
rs7162579	TTC23	cis	cerebellum	SCAN
rs7162579	SYNM	cis	parietal	SCAN
rs7162579	SYNM	cis	cerebellum	SCAN
rs7162579	TTC23	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99646800-99663600	Weak transcription	Ovary	ovary
2	chr15:99646800-99663600	Weak transcription	Spleen	Spleen
3	chr15:99647600-99672400	Weak transcription	Esophagus	oesophagus
4	chr15:99649000-99663800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:99650400-99663400	Weak transcription	HSMMtube	muscle
6	chr15:99650600-99663400	Weak transcription	Colonic Mucosa	Colon
7	chr15:99651200-99663800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:99652000-99669800	Weak transcription	Thymus	Thymus
9	chr15:99652200-99663600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:99654200-99663600	Weak transcription	Pancreas	Pancrea
11	chr15:99655400-99664400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr15:99656200-99663400	Enhancers	Rectal Smooth Muscle	rectum
13	chr15:99657800-99663600	Weak transcription	Gastric	stomach
14	chr15:99658600-99663400	Enhancers	Fetal Heart	heart
15	chr15:99660400-99663600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:99660600-99663600	Enhancers	Brain Hippocampus Middle	brain
17	chr15:99660600-99671600	Weak transcription	Liver	Liver
18	chr15:99661000-99663600	Weak transcription	Placenta	Placenta
19	chr15:99661000-99666400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:99661200-99663600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:99661200-99663600	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr15:99661600-99663400	Weak transcription	Right Ventricle	heart
23	chr15:99661600-99663600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:99661600-99663600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:99661600-99663600	Enhancers	Brain Anterior Caudate	brain
26	chr15:99661600-99663600	Enhancers	Brain Cingulate Gyrus	brain
27	chr15:99661800-99663600	Weak transcription	Fetal Thymus	thymus
28	chr15:99661800-99663600	Weak transcription	Right Atrium	heart
29	chr15:99662000-99663800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr15:99662000-99663800	Enhancers	Fetal Stomach	stomach
31	chr15:99662200-99663600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:99662200-99664000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:99662600-99666600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:99662800-99663600	Enhancers	Left Ventricle	heart
35	chr15:99662800-99663800	Enhancers	Fetal Muscle Trunk	muscle
36	chr15:99662800-99664200	Weak transcription	Fetal Kidney	kidney
37	chr15:99662800-99665600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:99662800-99666200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr15:99663000-99663400	Enhancers	HMEC	breast
40	chr15:99663000-99663400	Enhancers	NHDF-Ad	bronchial
41	chr15:99663000-99663600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr15:99663000-99663800	Enhancers	Brain Substantia Nigra	brain
43	chr15:99663200-99663400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:99663200-99663400	Weak transcription	Lung	lung
45	chr15:99663200-99663600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:99663200-99663600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:99663200-99663600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:99663200-99663600	Enhancers	Muscle Satellite Cultured Cells	--
49	chr15:99663200-99663600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:99663200-99663600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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