Variant report

Variant	rs56894248
Chromosome Location	chr2:46688264-46688265
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46593545..46595636-chr2:46687242..46688788,2	MCF-7	breast:
2	chr2:46673194..46677108-chr2:46685172..46689084,4	MCF-7	breast:
3	chr2:46561048..46561822-chr2:46688208..46689083,4	MCF-7	breast:
4	chr2:46591734..46592648-chr2:46688138..46688776,3	MCF-7	breast:
5	chr2:46236576..46237543-chr2:46688264..46688946,2	K562	blood:
6	chr2:46219810..46222412-chr2:46687121..46689791,4	MCF-7	breast:
7	chr2:46219968..46221252-chr2:46688230..46688933,7	MCF-7	breast:
8	chr2:46237659..46238661-chr2:46688156..46689453,6	K562	blood:
9	chr2:46305890..46306846-chr2:46688252..46689134,2	K562	blood:
10	chr2:46654324..46657409-chr2:46685735..46688601,3	K562	blood:
11	chr2:46679860..46680421-chr2:46688244..46689196,2	K562	blood:
12	chr2:46237923..46238577-chr2:46688234..46688787,2	MCF-7	breast:
13	chr2:46593059..46594102-chr2:46688159..46689154,5	MCF-7	breast:
14	chr2:46636115..46638908-chr2:46687157..46689113,2	MCF-7	breast:
15	chr2:46220268..46221206-chr2:46687774..46688837,4	K562	blood:
16	chr2:46561139..46561747-chr2:46688216..46688974,2	MCF-7	breast:
17	chr2:46237778..46238646-chr2:46688238..46688812,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000187600	Chromatin interaction
ENSG00000232696	Chromatin interaction
ENSG00000241791	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11125078	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11125081	0.80[EUR][1000 genomes]
rs12470939	0.89[EUR][1000 genomes]
rs12471274	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12472120	0.83[AMR][1000 genomes]
rs12473673	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12474961	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12474965	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12475015	0.90[ASN][1000 genomes]
rs12612916	0.86[EUR][1000 genomes]
rs12613088	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12613600	0.80[EUR][1000 genomes]
rs12617193	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619386	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12619696	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12619754	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12621486	0.92[EUR][1000 genomes]
rs12622818	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1530623	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1551123	0.94[EUR][1000 genomes]
rs1562454	0.94[EUR][1000 genomes]
rs17035200	0.92[EUR][1000 genomes]
rs1868095	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1868845	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2053766	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2121699	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2166746	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2276556	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2881326	0.86[EUR][1000 genomes]
rs34405528	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35589072	0.92[EUR][1000 genomes]
rs4145835	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4952825	0.85[ASN][1000 genomes]
rs4952826	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4952827	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4953364	0.92[EUR][1000 genomes]
rs4953370	0.89[EUR][1000 genomes]
rs4953376	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4953395	0.92[EUR][1000 genomes]
rs55871716	0.92[EUR][1000 genomes]
rs57720200	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs57996107	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58402726	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58725320	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59013670	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59761895	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59856996	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60685999	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61193538	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61560601	0.90[ASN][1000 genomes]
rs66533451	0.92[EUR][1000 genomes]
rs6714240	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6723195	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67739992	0.92[EUR][1000 genomes]
rs67960524	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68030749	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72618620	0.86[EUR][1000 genomes]
rs72618621	0.86[EUR][1000 genomes]
rs72618622	0.89[EUR][1000 genomes]
rs72618623	0.89[EUR][1000 genomes]
rs72618624	0.89[EUR][1000 genomes]
rs72618625	0.89[EUR][1000 genomes]
rs72618626	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72618627	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72618628	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72618629	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72618631	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72618632	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72873772	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7573688	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7574467	0.89[EUR][1000 genomes]
rs7595513	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9710956	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv581745	chr2:46660445-46693963	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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
14	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

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46667000-46688400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:46685800-46688400	Enhancers	Stomach Smooth Muscle	stomach
3	chr2:46685800-46688600	Enhancers	Fetal Stomach	stomach
4	chr2:46686000-46688600	Enhancers	Fetal Lung	lung
5	chr2:46686000-46689000	Enhancers	Adipose Nuclei	Adipose
6	chr2:46686200-46688600	Enhancers	Fetal Muscle Leg	muscle
7	chr2:46686200-46688800	Enhancers	Fetal Muscle Trunk	muscle
8	chr2:46686400-46688600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:46686400-46688600	Enhancers	Colon Smooth Muscle	Colon
10	chr2:46686400-46689000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:46686400-46689000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:46686400-46689000	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr2:46686400-46689200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr2:46686400-46689200	Enhancers	Right Atrium	heart
15	chr2:46686400-46689400	Enhancers	Lung	lung
16	chr2:46686400-46704400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:46686600-46688400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:46686600-46688600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:46686600-46688600	Enhancers	Fetal Intestine Large	intestine
20	chr2:46686600-46689000	Enhancers	Duodenum Mucosa	Duodenum
21	chr2:46686600-46689000	Enhancers	NHLF	lung
22	chr2:46686800-46688600	Enhancers	Fetal Heart	heart
23	chr2:46686800-46691600	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr2:46687000-46689000	Enhancers	Pancreas	Pancrea
25	chr2:46687000-46689200	Enhancers	Hela-S3	cervix
26	chr2:46687200-46688600	Enhancers	Left Ventricle	heart
27	chr2:46687200-46688600	Enhancers	Rectal Smooth Muscle	rectum
28	chr2:46687200-46688600	Enhancers	Right Ventricle	heart
29	chr2:46687200-46688600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr2:46687200-46689000	Enhancers	Stomach Mucosa	stomach
31	chr2:46687200-46689200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:46687200-46690600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:46687400-46688600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:46687400-46688600	Enhancers	Brain Angular Gyrus	brain
35	chr2:46687400-46688600	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr2:46687400-46688600	Enhancers	Brain Germinal Matrix	brain
37	chr2:46687400-46688600	Enhancers	Fetal Brain Female	brain
38	chr2:46687400-46688600	Enhancers	Gastric	stomach
39	chr2:46687400-46688600	Enhancers	Spleen	Spleen
40	chr2:46687400-46689000	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr2:46687400-46689000	Enhancers	Ovary	ovary
42	chr2:46687400-46689200	Enhancers	Placenta	Placenta
43	chr2:46687600-46688600	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr2:46687600-46688600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr2:46687600-46688800	Flanking Active TSS	HepG2	liver
46	chr2:46687600-46691600	Enhancers	NHDF-Ad	bronchial
47	chr2:46687600-46691800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:46687800-46688400	Weak transcription	Fetal Kidney	kidney
49	chr2:46687800-46688600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:46687800-46688600	Enhancers	Brain Inferior Temporal Lobe	brain

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