Variant report

Variant	rs3087657
Chromosome Location	chr15:44063859-44063860
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:44053208..44055542-chr15:44063582..44065145,2	K562	blood:
2	chr15:44061265..44064131-chr15:44066362..44068342,4	K562	blood:
3	chr15:44063293..44066887-chr15:44068416..44071024,5	K562	blood:
4	chr15:44060010..44065607-chr15:44066577..44070669,7	K562	blood:
5	chr15:44062113..44074982-chr15:44088756..44097846,29	MCF-7	breast:
6	chr15:44052819..44056366-chr15:44062691..44065082,4	K562	blood:
7	chr15:44062639..44065303-chr15:44085346..44088406,3	MCF-7	breast:
8	chr15:44060550..44065898-chr15:44066868..44071265,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000242028	Chromatin interaction
ENSG00000140264	Chromatin interaction
ENSG00000221792	Chromatin interaction
ENSG00000128886	Chromatin interaction
ENSG00000184716	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10518820	0.81[JPT][hapmap]
rs1053492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070410	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11070412	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11638972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12899922	0.85[AMR][1000 genomes]
rs12908467	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1975364	0.88[EUR][1000 genomes]
rs2016837	0.85[ASW][hapmap]
rs2260160	0.83[CHD][hapmap]
rs2411284	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2412822	0.85[ASW][hapmap]
rs2412823	0.84[ASW][hapmap];0.82[CEU][hapmap];0.89[LWK][hapmap]
rs2470135	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2918945	0.85[ASW][hapmap]
rs2927071	0.95[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2927085	0.86[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2955969	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3097773	0.81[JPT][hapmap]
rs35654783	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35866764	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4332723	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4617832	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4924720	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4924722	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs524908	0.92[ASW][hapmap];1.00[CEU][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap]
rs533143	1.00[CEU][hapmap];0.80[TSI][hapmap]
rs563940	0.85[ASW][hapmap]
rs575082	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs597705	0.85[ASW][hapmap]
rs62018947	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62018952	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs663214	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs667476	0.91[CEU][hapmap]
rs678513	0.85[ASW][hapmap]
rs686666	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs688009	0.95[CEU][hapmap]
rs693919	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs694461	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7174732	0.84[EUR][1000 genomes]
rs7175129	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7178343	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7180818	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8033995	0.82[JPT][hapmap]
rs8034451	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking 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	84 gene(s)	inside rSNPs	diseases
5	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
9	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
10	esv33661	chr15:44016519-44064420	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv1036318	chr15:44053617-44160773	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs3087657	STRC	cis	multi-tissue	Pritchard
rs3087657	ZSCAN29	cis	Thyroid	GTEx
rs3087657	STRCP1	cis	Thyroid	GTEx
rs3087657	DUOX2	cis	parietal	SCAN
rs3087657	TGM5	cis	Lymphoblastoid	GTEx
rs3087657	PATL2	cis	cerebellum	SCAN
rs3087657	STRCP1	cis	Whole Blood	GTEx
rs3087657	CKMT1A	cis	Esophagus Mucosa	GTEx
rs3087657	ADAL	cis	parietal	SCAN
rs3087657	WDR76	cis	parietal	SCAN
rs3087657	C15orf43	cis	cerebellum	SCAN
rs3087657	ZNF690	cis	multi-tissue	Pritchard
rs3087657	TGM5	cis	lymphoblastoid	seeQTL
rs3087657	AC011330.5	cis	Thyroid	GTEx
rs3087657	AC011330.5	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44041000-44068800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:44042000-44066600	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr15:44042000-44066800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr15:44042000-44067000	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:44042200-44067000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr15:44042600-44066600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:44043000-44066800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:44043400-44066600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:44043400-44066600	Strong transcription	Fetal Thymus	thymus
10	chr15:44043400-44066800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr15:44043400-44066800	Strong transcription	Placenta	Placenta
12	chr15:44043400-44067000	Strong transcription	Osteobl	bone
13	chr15:44043400-44067200	Strong transcription	HSMM	muscle
14	chr15:44043600-44066600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:44043600-44066800	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr15:44043800-44066800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:44044000-44066600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:44044000-44067000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:44044400-44065600	Strong transcription	HUVEC	blood vessel
20	chr15:44044400-44066600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:44044400-44068200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:44044600-44065600	Strong transcription	Brain Anterior Caudate	brain
23	chr15:44044600-44066400	Strong transcription	Adipose Nuclei	Adipose
24	chr15:44044600-44067000	Strong transcription	Fetal Intestine Large	intestine
25	chr15:44044800-44065600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:44044800-44065600	Strong transcription	Dnd41	blood
27	chr15:44044800-44066600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:44045000-44065800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr15:44045000-44067000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr15:44045000-44067200	Strong transcription	Fetal Stomach	stomach
31	chr15:44045200-44066400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:44045200-44066600	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr15:44045200-44066800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr15:44045200-44067200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:44045600-44065200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr15:44045600-44065800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:44045600-44066600	Strong transcription	Liver	Liver
38	chr15:44045800-44065800	Strong transcription	Left Ventricle	heart
39	chr15:44045800-44065800	Strong transcription	Thymus	Thymus
40	chr15:44045800-44066400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr15:44046000-44064400	Strong transcription	Colonic Mucosa	Colon
42	chr15:44046000-44065400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:44046000-44068000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:44046800-44066000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:44046800-44066800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr15:44047000-44065600	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr15:44047000-44066400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr15:44047200-44066400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:44047600-44066400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr15:44048200-44065600	Strong transcription	Muscle Satellite Cultured Cells	--

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