Variant report

Variant	rs56140081
Chromosome Location	chr3:99675181-99675182
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1038295	0.87[ASN][1000 genomes]
rs10804762	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485299	0.83[ASN][1000 genomes]
rs12486901	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487173	1.00[AFR][1000 genomes]
rs12489030	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491153	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12493124	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12493320	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1492343	0.83[ASN][1000 genomes]
rs1871847	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35590972	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732444	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3921767	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928152	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4928222	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55874130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55881709	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs55964918	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56223679	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56260910	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56335268	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60119031	0.90[ASN][1000 genomes]
rs61010376	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789694	1.00[AFR][1000 genomes]
rs6792339	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800456	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73858966	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73859911	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73860464	0.83[ASN][1000 genomes]
rs73860470	0.86[ASN][1000 genomes]
rs7632345	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635633	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7635871	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99657600-99686600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:99664600-99676200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:99664800-99677200	Weak transcription	Esophagus	oesophagus
4	chr3:99664800-99677200	Weak transcription	Ovary	ovary
5	chr3:99665000-99677200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:99665000-99677200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:99665000-99678800	Weak transcription	Aorta	Aorta
8	chr3:99669200-99679800	Weak transcription	Fetal Intestine Small	intestine
9	chr3:99670400-99676000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:99670800-99679200	Weak transcription	Small Intestine	intestine
11	chr3:99671400-99679400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:99671600-99684200	Weak transcription	NHEK	skin
13	chr3:99671600-99688200	Weak transcription	Primary T cells from cord blood	blood
14	chr3:99671800-99676400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:99672000-99678400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr3:99672000-99678400	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr3:99672600-99676800	Enhancers	HepG2	liver
18	chr3:99672600-99680000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:99672800-99675800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:99672800-99676600	Weak transcription	NHDF-Ad	bronchial
21	chr3:99672800-99677200	Weak transcription	Fetal Heart	heart
22	chr3:99672800-99677200	Weak transcription	Right Ventricle	heart
23	chr3:99672800-99680000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:99673000-99675600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:99673000-99676000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:99673000-99679400	Weak transcription	Osteobl	bone
27	chr3:99673000-99680800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:99673000-99681000	Weak transcription	HSMM	muscle
29	chr3:99673200-99675400	Weak transcription	Psoas Muscle	Psoas
30	chr3:99673200-99676000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:99673200-99676000	Weak transcription	HSMMtube	muscle
32	chr3:99673200-99677200	Weak transcription	Left Ventricle	heart
33	chr3:99673600-99675200	Enhancers	A549	lung
34	chr3:99673600-99676200	Enhancers	Stomach Mucosa	stomach
35	chr3:99674000-99675200	Flanking Active TSS	Liver	Liver
36	chr3:99674600-99676200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:99674600-99676200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:99674600-99677200	Weak transcription	Fetal Lung	lung
39	chr3:99674800-99675600	Enhancers	Pancreas	Pancrea
40	chr3:99675000-99675200	Enhancers	Gastric	stomach
41	chr3:99675000-99675400	Weak transcription	Right Atrium	heart
42	chr3:99675000-99676000	Weak transcription	Fetal Kidney	kidney

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