Variant report

Variant	rs10519757
Chromosome Location	chr15:33151410-33151411
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10152742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11071992	0.96[EUR][1000 genomes]
rs11632403	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1869034	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3887107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8032931	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422296	chr15:32798938-33221215	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv482680	chr15:32958401-33154005	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv832962	chr15:33111517-33239736	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv903978	chr15:33144202-33308641	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv1041609	chr15:33148035-33355999	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS 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	4 gene(s)	inside rSNPs	diseases
9	nsv542339	chr15:33148035-33355999	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv903980	chr15:33149087-33264201	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10519757	GREM1	cis	parietal	SCAN
rs10519757	FMN1	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33096200-33154000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr15:33096400-33159000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr15:33118600-33159000	Weak transcription	Gastric	stomach
4	chr15:33131200-33153800	Weak transcription	Fetal Kidney	kidney
5	chr15:33131800-33164800	Weak transcription	Pancreas	Pancrea
6	chr15:33132400-33154000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:33132800-33154000	Weak transcription	Brain Angular Gyrus	brain
8	chr15:33137800-33153600	Weak transcription	Fetal Thymus	thymus
9	chr15:33138800-33190600	Weak transcription	Thymus	Thymus
10	chr15:33139600-33190600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:33142600-33168200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:33144000-33153600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr15:33147000-33191400	Weak transcription	Lung	lung
14	chr15:33147400-33152200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:33148000-33158600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr15:33148400-33153800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr15:33148600-33153800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr15:33148600-33153800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:33148800-33153400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:33148800-33153800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr15:33148800-33153800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:33149000-33153400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr15:33149000-33153600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:33149000-33153600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr15:33149000-33153600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr15:33149000-33153800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr15:33149000-33153800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:33149000-33158800	Weak transcription	Hela-S3	cervix
29	chr15:33149000-33202000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr15:33149200-33153600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:33149200-33153600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:33149200-33153800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr15:33149200-33158800	Weak transcription	Stomach Mucosa	stomach
34	chr15:33149400-33152600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:33149400-33152800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:33149400-33153400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:33149400-33153400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:33149400-33153600	Weak transcription	Placenta	Placenta
39	chr15:33149400-33153800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr15:33149400-33153800	Enhancers	HSMMtube	muscle
41	chr15:33149400-33154200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr15:33149400-33159000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:33149600-33153400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:33149600-33153400	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr15:33149600-33153800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr15:33149600-33169600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr15:33149800-33153400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:33149800-33154000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:33150000-33151800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr15:33150000-33153600	Weak transcription	NH-A	brain

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