Variant report

Variant	rs1869034
Chromosome Location	chr15:33144202-33144203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10152742	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10519757	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]
rs11071992	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11632403	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3887107	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8032931	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];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1869034	GREM1	cis	parietal	SCAN
rs1869034	FMN1	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

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	chr15:33132000-33148600	Weak transcription	Stomach Mucosa	stomach
7	chr15:33132400-33154000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr15:33132800-33154000	Weak transcription	Brain Angular Gyrus	brain
9	chr15:33133000-33148200	Weak transcription	Esophagus	oesophagus
10	chr15:33133000-33150400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:33135800-33148200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:33137800-33153600	Weak transcription	Fetal Thymus	thymus
13	chr15:33138800-33190600	Weak transcription	Thymus	Thymus
14	chr15:33139600-33145800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:33139600-33190600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr15:33141600-33145200	Enhancers	Osteobl	bone
17	chr15:33141600-33145400	Enhancers	NHLF	lung
18	chr15:33141600-33145600	Enhancers	NHDF-Ad	bronchial
19	chr15:33141800-33146000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr15:33142000-33145200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:33142000-33145200	Enhancers	HSMM	muscle
22	chr15:33142000-33146200	Enhancers	HMEC	breast
23	chr15:33142200-33144400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:33142200-33144600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:33142200-33145200	Enhancers	HUVEC	blood vessel
26	chr15:33142200-33145400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:33142200-33145400	Enhancers	Hela-S3	cervix
28	chr15:33142200-33145600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:33142200-33145600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:33142200-33145600	Enhancers	NHEK	skin
31	chr15:33142600-33144400	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr15:33142600-33168200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:33143000-33144400	Enhancers	A549	lung
34	chr15:33143200-33146200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:33143200-33148600	Weak transcription	Placenta	Placenta
36	chr15:33143400-33144400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:33143400-33144600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:33143400-33145200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:33143400-33150000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:33143600-33144600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:33143600-33145000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr15:33143800-33146200	Enhancers	HepG2	liver
43	chr15:33143800-33147800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr15:33144000-33144600	Genic enhancers	HSMMtube	muscle
45	chr15:33144000-33153600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr15:33144200-33144400	Flanking Active TSS	NH-A	brain
47	chr15:33144200-33146800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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