Variant report

Variant	rs6440060
Chromosome Location	chr3:141762853-141762854
allele	A/T
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]
rs10935453	0.94[ASN][1000 genomes]
rs11706480	0.92[ASN][1000 genomes]
rs11714792	0.81[ASN][1000 genomes]
rs12496412	0.94[ASN][1000 genomes]
rs13065446	0.91[ASN][1000 genomes]
rs1355438	0.94[CEU][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1397764	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1511299	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1704985	0.91[EUR][1000 genomes]
rs1705607	0.91[EUR][1000 genomes]
rs1705614	0.88[EUR][1000 genomes]
rs1705624	0.89[EUR][1000 genomes]
rs2861422	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2862125	0.96[ASN][1000 genomes]
rs34186890	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34392664	0.92[ASN][1000 genomes]
rs347685	0.91[EUR][1000 genomes]
rs347686	0.91[EUR][1000 genomes]
rs347692	0.92[EUR][1000 genomes]
rs4683658	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440057	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6773343	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs6781340	0.92[ASN][1000 genomes]
rs6791514	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6794342	0.86[ASN][1000 genomes]
rs72990266	0.83[ASN][1000 genomes]
rs7630893	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7644155	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7644383	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9848817	0.95[ASN][1000 genomes]
rs9857917	0.87[EUR][1000 genomes]
rs9865413	0.89[EUR][1000 genomes]
rs9877536	0.92[ASN][1000 genomes]
rs9877817	0.94[CEU][hapmap];0.89[EUR][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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1002446	chr3:141719169-142070290	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv2757892	chr3:141728870-142129836	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	esv2759182	chr3:141728870-142129836	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv877553	chr3:141732321-141786073	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv877554	chr3:141735532-141781890	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv877555	chr3:141740076-141791408	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	esv2757013	chr3:141756541-142094631	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141747600-141773000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:141747600-141780400	Weak transcription	Left Ventricle	heart
3	chr3:141751200-141765000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr3:141751400-141764400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:141753600-141768400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:141755200-141771400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:141758400-141777400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:141758800-141768800	Weak transcription	Esophagus	oesophagus
9	chr3:141758800-141775800	Weak transcription	Ovary	ovary
10	chr3:141760000-141770000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:141760400-141763600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:141760400-141773800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:141760600-141763800	Weak transcription	Right Ventricle	heart
14	chr3:141760600-141764000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:141760600-141800800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:141760800-141772600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:141760800-141774600	Weak transcription	Liver	Liver
18	chr3:141761000-141772600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:141761000-141773400	Weak transcription	Dnd41	blood
20	chr3:141761000-141781600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:141761000-141807800	Weak transcription	Fetal Lung	lung
22	chr3:141761600-141772200	Weak transcription	Adipose Nuclei	Adipose
23	chr3:141761600-141775600	Weak transcription	NHEK	skin
24	chr3:141761800-141819600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:141762000-141772800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:141762200-141763000	Strong transcription	Thymus	Thymus
27	chr3:141762400-141763000	ZNF genes & repeats	Fetal Brain Female	brain
28	chr3:141762400-141763000	Strong transcription	Fetal Intestine Large	intestine
29	chr3:141762400-141763000	ZNF genes & repeats	Fetal Thymus	thymus
30	chr3:141762400-141763400	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr3:141762600-141763000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:141762600-141763000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
33	chr3:141762600-141763000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
34	chr3:141762600-141763000	ZNF genes & repeats	Aorta	Aorta
35	chr3:141762600-141763000	ZNF genes & repeats	Brain Germinal Matrix	brain
36	chr3:141762600-141763000	ZNF genes & repeats	Fetal Muscle Leg	muscle
37	chr3:141762600-141763000	ZNF genes & repeats	Fetal Stomach	stomach
38	chr3:141762600-141763000	ZNF genes & repeats	Pancreas	Pancrea
39	chr3:141762600-141763000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
40	chr3:141762600-141775800	Weak transcription	Lung	lung
41	chr3:141762800-141763000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
42	chr3:141762800-141763000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:141762800-141763200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:141762800-141782800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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