Variant report

Variant	rs12999586
Chromosome Location	chr2:46938736-46938737
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46925582..46927235-chr2:46936879..46939303,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CRIPT-4	chr2:46938723-46939649	ucscGeneNc_uc002rvj_1

Variant related genes	Relation type
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1058157	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1109380	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11676737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11695058	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12474201	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12998753	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12998762	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13012099	0.81[EUR][1000 genomes]
rs13025595	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13025984	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13031872	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13429704	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17822019	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17822294	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2346878	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34401107	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35158352	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35722922	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35825831	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3829835	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4952842	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4952843	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4953419	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4953423	0.81[EUR][1000 genomes]
rs6738426	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7562173	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7584870	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs7594523	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs897530	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	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

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46927800-46940000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr2:46928000-46943600	Weak transcription	Thymus	Thymus
3	chr2:46928600-46944400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:46928800-46946200	Weak transcription	NHEK	skin
5	chr2:46929000-46940200	Weak transcription	Fetal Stomach	stomach
6	chr2:46931200-46938800	Weak transcription	Primary B cells from cord blood	blood
7	chr2:46932400-46938800	Weak transcription	Primary T cells from cord blood	blood
8	chr2:46932600-46944200	Weak transcription	Aorta	Aorta
9	chr2:46933000-46943600	Weak transcription	Left Ventricle	heart
10	chr2:46934000-46944200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:46934000-46947800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:46934400-46943600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:46934600-46946400	Weak transcription	HSMM	muscle
14	chr2:46935200-46944000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:46936000-46941400	Weak transcription	Liver	Liver
16	chr2:46936000-46945000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:46936400-46940200	Weak transcription	Psoas Muscle	Psoas
18	chr2:46936400-46942200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:46936400-46943600	Weak transcription	Pancreas	Pancrea
20	chr2:46936600-46939800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:46936600-46943600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:46936800-46938800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:46936800-46942800	Weak transcription	NH-A	brain
24	chr2:46936800-46946200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:46937000-46938800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:46937000-46943800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:46937000-46944000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:46937000-46944200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:46937600-46943600	Weak transcription	Ovary	ovary
30	chr2:46937800-46939200	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr2:46938000-46938800	Genic enhancers	NHDF-Ad	bronchial
32	chr2:46938400-46938800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr2:46938400-46939400	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:46938600-46938800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:46938600-46939200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
36	chr2:46938600-46941200	Weak transcription	Osteobl	bone
37	chr2:46938600-46942600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:46938600-46943600	Weak transcription	NHLF	lung

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