Variant report

Variant	rs1869836
Chromosome Location	chr2:46882393-46882394
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46873644..46875189-chr2:46880714..46882765,2	MCF-7	breast:
2	chr2:46880745..46883271-chr2:46889135..46890937,2	MCF-7	breast:
3	chr2:46881672..46884638-chr2:47005149..47007963,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10495934	0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs12105006	0.81[ASN][1000 genomes]
rs13406663	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17818399	0.80[CHB][hapmap]
rs2346419	0.90[CHB][hapmap]
rs2881504	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60786889	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6544909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6544910	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6712910	0.94[ASN][1000 genomes]
rs7560464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7605089	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs982395	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[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	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
7	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1869836	CRIPT	cis	multi-tissue	Pritchard
rs1869836	CRIPT	cis	lymphoblastoid	seeQTL
rs1869836	LOC728819	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46869400-46883400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:46870000-46891000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:46870200-46889600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:46872000-46883400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:46873400-46883400	Weak transcription	Right Ventricle	heart
6	chr2:46873400-46884000	Weak transcription	Brain Anterior Caudate	brain
7	chr2:46874600-46883600	Weak transcription	Placenta	Placenta
8	chr2:46877600-46883400	Weak transcription	Spleen	Spleen
9	chr2:46877600-46884400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:46878400-46884600	Enhancers	NHLF	lung
11	chr2:46879200-46883400	Weak transcription	Adipose Nuclei	Adipose
12	chr2:46879200-46883400	Weak transcription	HSMM	muscle
13	chr2:46879400-46883400	Weak transcription	Ovary	ovary
14	chr2:46879400-46884600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:46879800-46884800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:46880000-46883400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:46880000-46884800	Enhancers	Osteobl	bone
18	chr2:46880400-46883800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:46880600-46883400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:46880600-46884600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:46880800-46884800	Enhancers	Fetal Lung	lung
22	chr2:46881200-46882800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:46881200-46882800	Weak transcription	HSMMtube	muscle
24	chr2:46881400-46882400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:46881400-46883400	Weak transcription	Lung	lung
26	chr2:46881600-46882600	Weak transcription	NH-A	brain
27	chr2:46881600-46883400	Weak transcription	Right Atrium	heart
28	chr2:46881800-46882400	Enhancers	Brain Angular Gyrus	brain
29	chr2:46882200-46882400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:46882200-46882400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:46882200-46882400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr2:46882200-46882400	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:46882200-46882600	Enhancers	Fetal Brain Female	brain
34	chr2:46882200-46882800	Enhancers	Fetal Brain Male	brain
35	chr2:46882200-46883400	Enhancers	NHDF-Ad	bronchial
36	chr2:46882200-46884600	Enhancers	Colon Smooth Muscle	Colon
37	chr2:46882200-46884800	Enhancers	A549	lung

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