Variant report

Variant	rs8029732
Chromosome Location	chr15:99664174-99664175
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:99643707..99645442-chr15:99663437..99665092,2	MCF-7	breast:
2	chr15:99663432..99665582-chr15:99669095..99671723,2	MCF-7	breast:
3	chr15:99664100..99665791-chr15:99675684..99677549,2	MCF-7	breast:
4	chr15:99664166..99665904-chr15:99695053..99697897,2	MCF-7	breast:
5	chr15:99649749..99652063-chr15:99662679..99664537,2	MCF-7	breast:
6	chr15:99652267..99657709-chr15:99661798..99664247,5	MCF-7	breast:
7	chr15:99658366..99661719-chr15:99663030..99668142,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182253	Chromatin interaction
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12324825	0.82[CHB][hapmap]
rs12591477	0.82[CHB][hapmap]
rs1530920	0.81[MEX][hapmap]
rs1670237	0.81[CHD][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs1810091	0.84[CHD][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes]
rs1965866	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1965867	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2242076	0.84[AMR][1000 genomes]
rs56009713	0.81[ASN][1000 genomes]
rs7162579	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8032817	0.82[AMR][1000 genomes]
rs8037159	0.81[ASN][1000 genomes]
rs8038392	0.81[CHB][hapmap]
rs8038845	0.86[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs906760	0.83[AMR][1000 genomes];0.81[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
rs8029732	LYSMD4	cis	cerebellum	SCAN
rs8029732	SYNM	cis	parietal	SCAN
rs8029732	TTC23	cis	cerebellum	SCAN
rs8029732	TTC23	cis	parietal	SCAN
rs8029732	SYNM	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99647600-99672400	Weak transcription	Esophagus	oesophagus
2	chr15:99652000-99669800	Weak transcription	Thymus	Thymus
3	chr15:99655400-99664400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr15:99660600-99671600	Weak transcription	Liver	Liver
5	chr15:99661000-99666400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:99662600-99666600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:99662800-99664200	Weak transcription	Fetal Kidney	kidney
8	chr15:99662800-99665600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:99662800-99666200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr15:99663200-99664200	Flanking Active TSS	A549	lung
11	chr15:99663200-99664600	Flanking Active TSS	HUVEC	blood vessel
12	chr15:99663200-99665000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:99663200-99665000	Enhancers	Fetal Intestine Large	intestine
14	chr15:99663200-99665000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr15:99663200-99665200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr15:99663200-99665200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:99663200-99666200	Flanking Active TSS	Hela-S3	cervix
18	chr15:99663200-99666400	Enhancers	Fetal Brain Male	brain
19	chr15:99663200-99666400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr15:99663200-99666800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:99663200-99666800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
22	chr15:99663400-99664600	Enhancers	Stomach Mucosa	stomach
23	chr15:99663400-99664600	Flanking Active TSS	HMEC	breast
24	chr15:99663400-99664800	Enhancers	Fetal Lung	lung
25	chr15:99663400-99665000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:99663400-99665200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr15:99663400-99665800	Enhancers	Lung	lung
28	chr15:99663600-99664200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr15:99663600-99664200	Flanking Active TSS	Colonic Mucosa	Colon
30	chr15:99663600-99664400	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr15:99663600-99664400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:99663600-99664400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:99663600-99664400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:99663600-99664400	Flanking Active TSS	Brain Angular Gyrus	brain
35	chr15:99663600-99664400	Enhancers	Brain Germinal Matrix	brain
36	chr15:99663600-99664400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
37	chr15:99663600-99664400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:99663600-99664400	Active TSS	Psoas Muscle	Psoas
39	chr15:99663600-99664400	Flanking Active TSS	HepG2	liver
40	chr15:99663600-99664600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr15:99663600-99664600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr15:99663600-99664600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:99663600-99664600	Active TSS	Aorta	Aorta
44	chr15:99663600-99664600	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr15:99663600-99664600	Flanking Active TSS	Brain Cingulate Gyrus	brain
46	chr15:99663600-99664600	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr15:99663600-99664600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr15:99663600-99664600	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr15:99663600-99664600	Flanking Active TSS	NHEK	skin
50	chr15:99663600-99664600	Flanking Active TSS	NHLF	lung

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