Variant report

Variant	rs1810091
Chromosome Location	chr15:99665036-99665037
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	chr15:99658366..99661719-chr15:99663030..99668142,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182253	Chromatin interaction
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12324825	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12591477	0.81[CEU][hapmap];0.91[CHB][hapmap];0.83[EUR][1000 genomes]
rs12595385	0.81[CHB][hapmap]
rs12911794	0.87[ASN][1000 genomes]
rs12915572	0.81[ASN][1000 genomes]
rs1530920	0.81[CHD][hapmap];0.81[MEX][hapmap]
rs1670237	0.85[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1965866	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1965867	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2242076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2305446	0.84[AMR][1000 genomes]
rs28819101	0.81[EUR][1000 genomes]
rs34567778	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34878632	0.80[EUR][1000 genomes]
rs4965445	0.81[CHD][hapmap]
rs55905808	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56009713	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7162579	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7164548	0.95[CHB][hapmap]
rs8026991	0.82[CHB][hapmap]
rs8029732	0.84[CHD][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes]
rs8032817	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8037159	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8038392	0.85[CHB][hapmap]
rs8038845	0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8041213	0.89[ASN][1000 genomes]
rs896700	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs906760	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1810091	TTC23	cis	cerebellum	SCAN
rs1810091	SYNM	cis	parietal	SCAN
rs1810091	TTC23	cis	multi-tissue	Pritchard
rs1810091	SYNM	cis	cerebellum	SCAN
rs1810091	LYSMD4	cis	cerebellum	SCAN
rs1810091	TTC23	cis	parietal	SCAN

Chromatin state (count:101 , 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	chr15:99660600-99671600	Weak transcription	Liver	Liver
4	chr15:99661000-99666400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:99662600-99666600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:99662800-99665600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:99662800-99666200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr15:99663200-99665200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr15:99663200-99665200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:99663200-99666200	Flanking Active TSS	Hela-S3	cervix
11	chr15:99663200-99666400	Enhancers	Fetal Brain Male	brain
12	chr15:99663200-99666400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr15:99663200-99666800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:99663200-99666800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
15	chr15:99663400-99665200	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr15:99663400-99665800	Enhancers	Lung	lung
17	chr15:99663600-99665200	Enhancers	H1 Cell Line	embryonic stem cell
18	chr15:99663600-99665200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr15:99663600-99665200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:99663600-99665200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr15:99663600-99665200	Enhancers	Placenta Amnion	Placenta Amnion
22	chr15:99663600-99665400	Enhancers	Placenta	Placenta
23	chr15:99663600-99665600	Enhancers	Gastric	stomach
24	chr15:99663600-99665800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr15:99663600-99666000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:99663600-99667000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:99663600-99679400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr15:99664000-99666000	Flanking Active TSS	HSMMtube	muscle
29	chr15:99664000-99666200	Enhancers	Fetal Brain Female	brain
30	chr15:99664200-99665400	Flanking Active TSS	Rectal Smooth Muscle	rectum
31	chr15:99664200-99665600	Enhancers	K562	blood
32	chr15:99664200-99665800	Enhancers	Spleen	Spleen
33	chr15:99664200-99666200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr15:99664200-99666800	Enhancers	Fetal Muscle Trunk	muscle
35	chr15:99664200-99667200	Enhancers	Fetal Muscle Leg	muscle
36	chr15:99664200-99675800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:99664400-99665200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:99664400-99665200	Flanking Active TSS	Fetal Heart	heart
39	chr15:99664400-99665800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:99664400-99665800	Genic enhancers	Fetal Stomach	stomach
41	chr15:99664400-99665800	Enhancers	Ovary	ovary
42	chr15:99664400-99666000	Enhancers	Brain Angular Gyrus	brain
43	chr15:99664400-99666000	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr15:99664400-99666400	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr15:99664400-99666800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr15:99664400-99666800	Enhancers	Brain Substantia Nigra	brain
47	chr15:99664400-99667200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:99664400-99667400	Enhancers	Right Atrium	heart
49	chr15:99664400-99678800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:99664400-99678800	Weak transcription	Brain Germinal Matrix	brain

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