Variant report

Variant	rs56205540
Chromosome Location	chr3:120426401-120426402
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:120419207..120421176-chr3:120424501..120427081,2	K562	blood:
2	chr3:120400001..120401507-chr3:120424944..120426779,2	MCF-7	breast:
3	chr3:120417863..120420778-chr3:120426396..120428792,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113924	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs34793874	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56384839	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73183711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73183712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73183713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73183714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73183717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73183719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73183720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73183721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73183725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73183729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv877377	chr3:120287683-120426750	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
5	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120398200-120427000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:120398200-120427800	Weak transcription	Placenta	Placenta
3	chr3:120398200-120430200	Weak transcription	NHEK	skin
4	chr3:120398200-120438000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:120398800-120442200	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:120402800-120456600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:120405600-120436800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:120406400-120436600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:120408400-120429400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:120408600-120427400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:120411000-120436600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:120412800-120426600	Weak transcription	Brain Angular Gyrus	brain
13	chr3:120412800-120435600	Weak transcription	NH-A	brain
14	chr3:120412800-120438000	Weak transcription	Fetal Intestine Small	intestine
15	chr3:120415000-120438000	Weak transcription	HepG2	liver
16	chr3:120416400-120436800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:120416400-120437200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:120416400-120437800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:120416400-120460600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:120416600-120438000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:120416800-120460600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:120417000-120427600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:120417600-120456600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:120418800-120429400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:120419000-120450800	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:120420200-120428800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:120422000-120426600	Weak transcription	Aorta	Aorta
28	chr3:120422000-120427400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:120422000-120438000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:120422000-120438000	Weak transcription	Fetal Stomach	stomach
31	chr3:120422000-120438000	Weak transcription	Fetal Thymus	thymus
32	chr3:120422000-120438000	Weak transcription	Left Ventricle	heart
33	chr3:120422200-120437000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:120422200-120438000	Weak transcription	Adipose Nuclei	Adipose
35	chr3:120422200-120438000	Weak transcription	Fetal Kidney	kidney
36	chr3:120422200-120441000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:120422200-120446800	Weak transcription	Ovary	ovary
38	chr3:120422400-120437000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:120422400-120438000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:120422400-120444200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:120422600-120437800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:120423000-120433200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr3:120423000-120460200	Weak transcription	HUVEC	blood vessel
44	chr3:120423200-120427800	Weak transcription	Fetal Lung	lung
45	chr3:120423200-120437200	Weak transcription	GM12878-XiMat	blood
46	chr3:120423400-120428400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:120423400-120428400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr3:120423400-120429400	Weak transcription	Primary T cells from cord blood	blood
49	chr3:120423400-120437400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:120423400-120438000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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