Variant report

Variant	rs4399891
Chromosome Location	chr3:115718732-115718733
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	chr3:115718424..115720399-chr3:115727607..115730544,2	K562	blood:
2	chr3:115714015..115716158-chr3:115718030..115720877,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11918028	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485818	0.86[JPT][hapmap]
rs12495426	0.86[JPT][hapmap]
rs13065579	0.87[JPT][hapmap]
rs13086615	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1920382	0.86[JPT][hapmap]
rs1920383	0.86[JPT][hapmap]
rs1920384	0.86[JPT][hapmap]
rs1920388	0.83[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2141626	0.87[JPT][hapmap]
rs2141629	0.87[JPT][hapmap]
rs35764849	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4131452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4131453	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4240163	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4240164	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4240165	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4240166	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4286426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4315682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4378955	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4398428	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4426677	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4518124	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4599302	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4611819	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4831218	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4831219	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4831220	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4831221	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4831222	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4831223	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6438296	0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6776244	0.86[JPT][hapmap]
rs6777196	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6787687	0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787872	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs6789600	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790290	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6795318	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6804278	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6807809	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7610371	0.86[JPT][hapmap]
rs7625191	0.82[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7632252	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289033	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289034	0.92[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9289040	0.86[JPT][hapmap]
rs9813153	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs9815418	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9833319	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9840787	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9848298	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs9850406	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9863087	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs9869887	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9872913	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9873260	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9878286	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931948	chr3:114884574-115802562	Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2760762	chr3:115476222-115807650	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv829685	chr3:115643521-115812913	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1012260	chr3:115680931-115935968	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115717000-115718800	Enhancers	Brain Angular Gyrus	brain
2	chr3:115717200-115719000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:115717200-115719600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:115717400-115720400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr3:115717600-115718800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:115717800-115718800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:115717800-115718800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:115717800-115719000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr3:115717800-115719000	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr3:115717800-115719200	Enhancers	NHDF-Ad	bronchial
11	chr3:115717800-115719400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:115717800-115719400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:115717800-115719400	Weak transcription	Fetal Brain Male	brain
14	chr3:115717800-115719600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr3:115718000-115718800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:115718000-115718800	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr3:115718000-115718800	Enhancers	Brain Germinal Matrix	brain
18	chr3:115718000-115718800	Enhancers	NH-A	brain
19	chr3:115718000-115719400	Enhancers	NHEK	skin
20	chr3:115718000-115719600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:115718000-115719800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr3:115718000-115720200	Enhancers	HSMMtube	muscle
23	chr3:115718000-115721400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:115718000-115721400	Enhancers	HSMM	muscle
25	chr3:115718200-115719400	Enhancers	Brain Anterior Caudate	brain
26	chr3:115718200-115719600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:115718200-115719600	Enhancers	Fetal Muscle Leg	muscle
28	chr3:115718200-115720000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:115718200-115720000	Enhancers	K562	blood
30	chr3:115718200-115720600	Enhancers	NHLF	lung
31	chr3:115718200-115721800	Enhancers	Osteobl	bone
32	chr3:115718400-115718800	Weak transcription	Brain Substantia Nigra	brain
33	chr3:115718400-115719600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:115718400-115719800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:115718400-115720000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:115718400-115720000	Enhancers	GM12878-XiMat	blood
37	chr3:115718400-115721200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:115718400-115721400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:115718400-115721600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:115718400-115721800	Enhancers	HMEC	breast
41	chr3:115718400-115722800	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr3:115718600-115718800	Enhancers	H1 Cell Line	embryonic stem cell
43	chr3:115718600-115718800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr3:115718600-115719200	Enhancers	A549	lung
45	chr3:115718600-115719400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:115718600-115719400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:115718600-115719400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:115718600-115719400	Enhancers	Brain Hippocampus Middle	brain
49	chr3:115718600-115719800	Enhancers	Hela-S3	cervix
50	chr3:115718600-115721600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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