Variant report

Variant	rs56695029
Chromosome Location	chr1:46142718-46142719
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46141722..46144988-chr1:46150323..46153759,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159592	Chromatin interaction
ENSG00000159596	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs34965970	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35210931	1.00[AMR][1000 genomes]
rs57402001	1.00[AMR][1000 genomes]
rs57813129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59974520	1.00[AMR][1000 genomes]
rs60301454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60916630	0.83[AFR][1000 genomes]
rs60952228	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61169182	1.00[AMR][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	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
2	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
4	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
5	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv1014128	chr1:46097670-46394540	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46124800-46144600	Weak transcription	Aorta	Aorta
2	chr1:46125000-46148400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:46125200-46151000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:46126000-46143000	Weak transcription	Fetal Lung	lung
5	chr1:46126000-46143800	Weak transcription	Fetal Brain Female	brain
6	chr1:46126000-46144200	Weak transcription	Brain Germinal Matrix	brain
7	chr1:46126000-46145000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:46126000-46147200	Weak transcription	Thymus	Thymus
9	chr1:46126000-46149000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:46126000-46151000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:46126200-46144800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:46126200-46148600	Weak transcription	Fetal Stomach	stomach
13	chr1:46126400-46143000	Weak transcription	Primary T cells from cord blood	blood
14	chr1:46126400-46144200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:46126400-46144800	Weak transcription	Colonic Mucosa	Colon
16	chr1:46126400-46144800	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:46126400-46146600	Weak transcription	Fetal Kidney	kidney
18	chr1:46126400-46151000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:46126600-46143000	Weak transcription	Fetal Intestine Large	intestine
20	chr1:46126600-46144800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:46126600-46150600	Weak transcription	Placenta	Placenta
22	chr1:46126800-46145000	Weak transcription	HMEC	breast
23	chr1:46126800-46147200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:46127000-46143600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:46127000-46144800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:46127200-46143400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:46129200-46143000	Weak transcription	Primary B cells from cord blood	blood
28	chr1:46129400-46143400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:46132800-46142800	Weak transcription	Brain Anterior Caudate	brain
30	chr1:46133600-46143000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:46133800-46145000	Weak transcription	Brain Angular Gyrus	brain
32	chr1:46134200-46151000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:46135000-46143000	Weak transcription	Brain Substantia Nigra	brain
34	chr1:46135200-46144400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:46135200-46144800	Weak transcription	Ovary	ovary
36	chr1:46136000-46143400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:46136000-46143400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:46136000-46146400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:46136000-46150000	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:46136200-46143000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:46136200-46143000	Weak transcription	A549	lung
42	chr1:46136200-46143200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:46136400-46143000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:46136400-46143000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:46136400-46143000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:46136400-46143000	Weak transcription	HSMMtube	muscle
47	chr1:46136400-46143000	Weak transcription	NHLF	lung
48	chr1:46136400-46143000	Weak transcription	Osteobl	bone
49	chr1:46136400-46143200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:46136400-46144400	Weak transcription	NHDF-Ad	bronchial

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