Variant report

Variant	rs2881504
Chromosome Location	chr2:46879069-46879070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46878330..46881145-chr2:46885886..46887548,2	MCF-7	breast:
2	chr2:46878154..46881998-chr2:46882962..46887664,5	K562	blood:
3	chr2:46858190..46860750-chr2:46875566..46879072,3	MCF-7	breast:
4	chr2:46872845..46875146-chr2:46877009..46879600,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CRIPT-1	chr2:46878783-46879262	NONHSAT070518

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10495934	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[ASN][1000 genomes]
rs13406663	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17818399	0.80[CHB][hapmap]
rs1869836	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2346419	0.90[CHB][hapmap]
rs60786889	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6544909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6544910	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6712910	0.96[ASN][1000 genomes]
rs7560464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7605089	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs982395	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2881504	CRIPT	cis	multi-tissue	Pritchard

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	chr2:46869600-46881200	Weak transcription	Primary T cells from cord blood	blood
3	chr2:46869800-46882200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:46870000-46880800	Weak transcription	Primary B cells from cord blood	blood
5	chr2:46870000-46891000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:46870200-46889600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:46872000-46883400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:46873000-46880600	Weak transcription	Right Atrium	heart
9	chr2:46873200-46879800	Weak transcription	Psoas Muscle	Psoas
10	chr2:46873400-46881800	Weak transcription	Brain Angular Gyrus	brain
11	chr2:46873400-46883400	Weak transcription	Right Ventricle	heart
12	chr2:46873400-46884000	Weak transcription	Brain Anterior Caudate	brain
13	chr2:46874000-46880400	Weak transcription	HSMMtube	muscle
14	chr2:46874600-46883600	Weak transcription	Placenta	Placenta
15	chr2:46875400-46880400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:46876000-46880000	Weak transcription	Osteobl	bone
17	chr2:46876400-46879400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:46876400-46879600	Weak transcription	HepG2	liver
19	chr2:46876600-46879800	Enhancers	A549	lung
20	chr2:46877200-46880600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:46877400-46879600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:46877600-46879400	Enhancers	Fetal Lung	lung
23	chr2:46877600-46883400	Weak transcription	Spleen	Spleen
24	chr2:46877600-46884400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:46878000-46879200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:46878000-46879600	Enhancers	NHDF-Ad	bronchial
27	chr2:46878000-46881200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:46878200-46879200	Enhancers	Adipose Nuclei	Adipose
29	chr2:46878200-46879800	Enhancers	Fetal Muscle Leg	muscle
30	chr2:46878400-46879400	Enhancers	Fetal Stomach	stomach
31	chr2:46878400-46884600	Enhancers	NHLF	lung
32	chr2:46878600-46879200	Enhancers	HSMM	muscle
33	chr2:46878600-46879400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:46878600-46879400	Enhancers	Stomach Smooth Muscle	stomach
35	chr2:46878800-46879200	Weak transcription	Ovary	ovary
36	chr2:46879000-46879200	Enhancers	Brain Cingulate Gyrus	brain
37	chr2:46879000-46879400	Weak transcription	Colon Smooth Muscle	Colon

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