Variant report

Variant	rs1562454
Chromosome Location	chr2:46721481-46721482
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46707494..46710484-chr2:46718946..46721502,2	K562	blood:
2	chr2:46715260..46716783-chr2:46718663..46721578,2	MCF-7	breast:
3	chr2:46721452..46724242-chr2:46727690..46730244,3	MCF-7	breast:
4	chr2:46721184..46729524-chr2:46766976..46775977,14	K562	blood:

Variant related genes	Relation type
ENSG00000250565	Chromatin interaction
ENSG00000119729	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11125078	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.89[EUR][1000 genomes]
rs11125079	0.84[YRI][hapmap]
rs11125080	0.89[YRI][hapmap]
rs11125081	0.88[GIH][hapmap];0.81[AMR][1000 genomes]
rs12470939	0.83[EUR][1000 genomes]
rs12471274	0.92[EUR][1000 genomes]
rs12473673	0.92[EUR][1000 genomes]
rs12474961	0.81[EUR][1000 genomes]
rs12474965	0.86[EUR][1000 genomes]
rs12612916	1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.86[EUR][1000 genomes]
rs12613088	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12613600	0.81[AMR][1000 genomes]
rs12617193	0.94[EUR][1000 genomes]
rs12619386	0.89[EUR][1000 genomes]
rs12619696	1.00[CEU][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs12619754	0.83[EUR][1000 genomes]
rs12621486	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12622818	0.86[MEX][hapmap];0.86[EUR][1000 genomes]
rs1530623	0.81[MEX][hapmap];0.83[EUR][1000 genomes]
rs1551123	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17035200	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1868845	0.92[EUR][1000 genomes]
rs2053766	0.83[EUR][1000 genomes]
rs2121699	0.89[EUR][1000 genomes]
rs2166746	0.83[EUR][1000 genomes]
rs2276556	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2881326	0.81[EUR][1000 genomes]
rs34405528	0.86[EUR][1000 genomes]
rs35589072	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4145835	0.83[EUR][1000 genomes]
rs4952826	1.00[CEU][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.92[EUR][1000 genomes]
rs4952827	1.00[CEU][hapmap];0.80[JPT][hapmap];0.92[EUR][1000 genomes]
rs4953364	0.86[MEX][hapmap];0.86[EUR][1000 genomes]
rs4953370	0.83[EUR][1000 genomes]
rs4953376	0.81[MEX][hapmap];0.83[EUR][1000 genomes]
rs4953395	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55871716	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56894248	0.94[EUR][1000 genomes]
rs57996107	0.92[EUR][1000 genomes]
rs58402726	0.89[EUR][1000 genomes]
rs58725320	0.89[EUR][1000 genomes]
rs59013670	0.86[EUR][1000 genomes]
rs59761895	0.89[EUR][1000 genomes]
rs59856996	0.94[EUR][1000 genomes]
rs60685999	0.94[EUR][1000 genomes]
rs61193538	0.92[EUR][1000 genomes]
rs66533451	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6714240	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6719900	0.81[CHD][hapmap]
rs6723195	0.86[EUR][1000 genomes]
rs6746695	1.00[CEU][hapmap]
rs6749107	0.81[CHD][hapmap]
rs67739992	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67960524	0.94[EUR][1000 genomes]
rs68030749	0.92[EUR][1000 genomes]
rs72618620	0.81[EUR][1000 genomes]
rs72618621	0.81[EUR][1000 genomes]
rs72618622	0.83[EUR][1000 genomes]
rs72618623	0.83[EUR][1000 genomes]
rs72618624	0.83[EUR][1000 genomes]
rs72618625	0.83[EUR][1000 genomes]
rs72618626	0.83[EUR][1000 genomes]
rs72618627	0.83[EUR][1000 genomes]
rs72618628	0.89[EUR][1000 genomes]
rs72618629	0.89[EUR][1000 genomes]
rs72618631	0.92[EUR][1000 genomes]
rs72618632	0.89[EUR][1000 genomes]
rs72873772	0.97[EUR][1000 genomes]
rs7573688	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7574467	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7595513	1.00[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv437435	chr2:46636967-46763587	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv9702	chr2:46668106-46745740	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv817828	chr2:46670146-46739157	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	nsv519216	chr2:46683683-46723219	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv457341	chr2:46712759-46724016	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv581748	chr2:46712759-46724016	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46714800-46721600	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr2:46718000-46722600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:46718200-46722600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:46718200-46726600	Weak transcription	Aorta	Aorta
5	chr2:46718400-46726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:46718600-46722000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:46718600-46722600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:46718600-46725600	Weak transcription	Brain Substantia Nigra	brain
9	chr2:46718600-46726600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr2:46718600-46726600	Weak transcription	Right Ventricle	heart
11	chr2:46718800-46722400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:46718800-46726400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:46718800-46726600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:46718800-46727000	Weak transcription	Spleen	Spleen
15	chr2:46720400-46721600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:46720400-46721600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:46720400-46721800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:46720400-46721800	Enhancers	Fetal Brain Female	brain
19	chr2:46720400-46722200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:46720600-46721600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:46720600-46722000	Enhancers	Brain Germinal Matrix	brain
22	chr2:46720600-46723400	Enhancers	Fetal Brain Male	brain
23	chr2:46720800-46722600	Weak transcription	HSMM	muscle
24	chr2:46721000-46721600	Enhancers	Brain Anterior Caudate	brain
25	chr2:46721000-46722600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:46721000-46722600	Weak transcription	NHDF-Ad	bronchial
27	chr2:46721000-46726600	Weak transcription	Colon Smooth Muscle	Colon
28	chr2:46721200-46721600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:46721200-46721600	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:46721200-46721600	Enhancers	GM12878-XiMat	blood
31	chr2:46721200-46721600	Enhancers	NHEK	skin
32	chr2:46721200-46722600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:46721200-46726600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:46721200-46726600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:46721200-46726600	Weak transcription	Left Ventricle	heart
36	chr2:46721400-46722400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:46721400-46722600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:46721400-46722600	Weak transcription	NH-A	brain
39	chr2:46721400-46722600	Weak transcription	Osteobl	bone
40	chr2:46721400-46722800	Weak transcription	NHLF	lung
41	chr2:46721400-46724800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:46721400-46725400	Weak transcription	Hela-S3	cervix
43	chr2:46721400-46726600	Weak transcription	Stomach Smooth Muscle	stomach

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