Variant report

Variant	rs56679555
Chromosome Location	chr1:209920272-209920273
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209920122..209922907-chr1:209973621..209976183,2	MCF-7	breast:
2	chr1:209897489..209898995-chr1:209918699..209920810,2	K562	blood:
3	chr1:209913450..209916086-chr1:209919671..209921571,2	K562	blood:
4	chr1:209916474..209918920-chr1:209920104..209922211,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236136	Chromatin interaction
ENSG00000117595	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10489341	0.85[ASN][1000 genomes]
rs11119333	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12024779	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12040780	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12075595	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17015053	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17015095	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015099	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57606822	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58627173	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60132042	0.93[ASN][1000 genomes]
rs61279558	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6680324	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089418	0.93[ASN][1000 genomes]
rs846909	0.93[ASN][1000 genomes]
rs846911	0.93[ASN][1000 genomes]
rs860185	0.93[ASN][1000 genomes]
rs861762	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1001588	chr1:209908876-209938243	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209907600-209920800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209915200-209920800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:209915200-209921000	Weak transcription	Spleen	Spleen
4	chr1:209915400-209920400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:209915400-209920800	Weak transcription	Esophagus	oesophagus
6	chr1:209915600-209920600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:209916000-209920800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:209916000-209920800	Weak transcription	GM12878-XiMat	blood
9	chr1:209916800-209920400	Weak transcription	Gastric	stomach
10	chr1:209916800-209920800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:209916800-209920800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:209916800-209920800	Weak transcription	Left Ventricle	heart
13	chr1:209917000-209920400	Weak transcription	Ovary	ovary
14	chr1:209917000-209920400	Weak transcription	HMEC	breast
15	chr1:209917000-209920600	Weak transcription	Brain Anterior Caudate	brain
16	chr1:209917000-209920800	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:209917000-209920800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:209917200-209920400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:209917200-209920600	Weak transcription	Osteobl	bone
20	chr1:209917200-209920800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:209917200-209920800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:209917200-209920800	Weak transcription	Liver	Liver
23	chr1:209917200-209920800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:209917200-209920800	Weak transcription	NH-A	brain
25	chr1:209917200-209920800	Weak transcription	NHLF	lung
26	chr1:209917800-209920800	Weak transcription	Pancreas	Pancrea
27	chr1:209917800-209920800	Weak transcription	Right Atrium	heart
28	chr1:209917800-209920800	Weak transcription	Right Ventricle	heart
29	chr1:209918400-209920800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:209918600-209920400	Weak transcription	Brain Angular Gyrus	brain
31	chr1:209918800-209920400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:209919000-209920400	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:209919400-209920800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:209919400-209921000	Enhancers	Fetal Intestine Large	intestine
35	chr1:209919600-209920600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:209919600-209920800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:209919600-209920800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:209919600-209922400	Enhancers	Fetal Heart	heart
39	chr1:209919800-209920600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:209919800-209920800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:209919800-209920800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:209919800-209921000	Weak transcription	Thymus	Thymus
43	chr1:209919800-209923400	Enhancers	Fetal Intestine Small	intestine
44	chr1:209920000-209920800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:209920000-209920800	Enhancers	Brain Cingulate Gyrus	brain
46	chr1:209920000-209920800	Enhancers	Stomach Mucosa	stomach
47	chr1:209920000-209920800	Enhancers	K562	blood
48	chr1:209920200-209920800	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr1:209920200-209920800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:209920200-209920800	Enhancers	Adipose Nuclei	Adipose

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