Variant report

Variant	rs56880774
Chromosome Location	chr3:143712214-143712215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143689616..143692176-chr3:143710763..143713243,2	K562	blood:
2	chr3:143694586..143698442-chr3:143710768..143713586,3	K562	blood:

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10513239	0.92[EUR][1000 genomes]
rs11720435	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11917772	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13317365	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13320111	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1604886	0.81[EUR][1000 genomes]
rs2370173	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28627639	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6776760	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73000690	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73002695	0.96[EUR][1000 genomes]
rs73002698	0.96[EUR][1000 genomes]
rs73872672	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7627966	0.96[EUR][1000 genomes]
rs7637012	0.81[EUR][1000 genomes]
rs964572	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9823162	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9834740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9835993	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9847681	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9849618	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9860540	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9861563	0.98[EUR][1000 genomes]
rs9870939	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9874033	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9876107	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9879081	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143692800-143714200	Weak transcription	Small Intestine	intestine
2	chr3:143693400-143713800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:143694400-143718800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:143694400-143719400	Weak transcription	Hela-S3	cervix
5	chr3:143695600-143716800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:143697000-143713400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:143697000-143722800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:143697000-143729200	Weak transcription	Aorta	Aorta
9	chr3:143697200-143723000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:143697200-143727800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:143698400-143721200	Weak transcription	Fetal Kidney	kidney
12	chr3:143699000-143717000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:143699200-143737600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:143699400-143714000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:143700400-143720400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:143702400-143717000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:143702600-143727400	Weak transcription	Pancreas	Pancrea
18	chr3:143703200-143720600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:143703400-143719400	Weak transcription	Placenta	Placenta
20	chr3:143704400-143716200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:143704600-143712400	Weak transcription	Gastric	stomach
22	chr3:143704600-143719600	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:143704600-143725800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:143705600-143722600	Weak transcription	Esophagus	oesophagus
25	chr3:143706000-143715000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:143706400-143712600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:143706400-143728000	Weak transcription	Fetal Stomach	stomach
28	chr3:143706600-143714000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:143706600-143722600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:143706800-143713200	Weak transcription	Thymus	Thymus
31	chr3:143706800-143725000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:143707000-143722600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:143707400-143714200	Weak transcription	Brain Anterior Caudate	brain
34	chr3:143707400-143714200	Weak transcription	Brain Substantia Nigra	brain
35	chr3:143707400-143714400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:143707400-143714600	Weak transcription	Brain Angular Gyrus	brain
37	chr3:143707800-143712600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:143707800-143713400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:143708000-143713600	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:143708000-143729200	Weak transcription	Ovary	ovary
41	chr3:143708800-143713400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:143708800-143716200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:143708800-143717200	Weak transcription	NHEK	skin
44	chr3:143708800-143720400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:143708800-143729200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:143709000-143714000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr3:143709000-143714000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:143709000-143714200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr3:143709000-143716800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:143709000-143720600	Weak transcription	Fetal Muscle Leg	muscle

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