Variant report

Variant	rs12546205
Chromosome Location	chr8:6421277-6421278
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11996740	1.00[CHB][hapmap]
rs12541109	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12543837	1.00[CHB][hapmap]
rs12547077	1.00[CHB][hapmap]
rs12547116	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12549365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17077573	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17553089	1.00[YRI][hapmap]
rs17553929	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17553964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17554274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs17623747	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[GIH][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs17623771	0.85[EUR][1000 genomes]
rs17624022	1.00[CHB][hapmap]
rs17624399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17624865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2442528	0.81[CHB][hapmap]
rs2442549	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2442550	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2442551	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2442585	1.00[YRI][hapmap]
rs2515514	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2922826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2922840	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2922841	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2922842	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2922843	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2922845	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2959776	0.89[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2959777	1.00[JPT][hapmap]
rs3739390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3739392	0.82[ASW][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs55993125	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56076232	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56112478	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73661407	1.00[EUR][1000 genomes]
rs7817104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7820827	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7832816	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7833871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7838154	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890034	chr8:5926632-6427868	Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3506199	chr8:6116693-6536592	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	esv3506200	chr8:6116693-6536592	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers 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	11 gene(s)	inside rSNPs	diseases
6	nsv933282	chr8:6261036-6440592	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1015981	chr8:6286575-6578450	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats 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	37 gene(s)	inside rSNPs	diseases
9	nsv890057	chr8:6317165-6427868	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1021684	chr8:6350091-6809455	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	esv2422383	chr8:6362389-6781593	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv610004	chr8:6402366-6772913	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv1029241	chr8:6411300-6761720	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6342400-6421400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr8:6364200-6478200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr8:6407800-6423800	Weak transcription	Spleen	Spleen
4	chr8:6415200-6424000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:6416400-6422200	Enhancers	Primary B cells from peripheral blood	blood
6	chr8:6416800-6442400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr8:6417600-6424000	Weak transcription	NHEK	skin
8	chr8:6417600-6442800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr8:6418600-6422600	Enhancers	HepG2	liver
10	chr8:6419000-6462400	Weak transcription	GM12878-XiMat	blood
11	chr8:6419400-6421400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr8:6419600-6423400	Weak transcription	Primary T cells from cord blood	blood
13	chr8:6419600-6423800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr8:6419800-6423600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr8:6420000-6427400	Weak transcription	Thymus	Thymus
16	chr8:6420200-6421400	Flanking Active TSS	HUVEC	blood vessel
17	chr8:6420600-6421600	Enhancers	Primary B cells from cord blood	blood
18	chr8:6420600-6421800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr8:6420600-6423800	Weak transcription	Pancreas	Pancrea
20	chr8:6420800-6421400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr8:6420800-6421600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr8:6420800-6421600	Weak transcription	Fetal Intestine Large	intestine
23	chr8:6420800-6423800	Weak transcription	Gastric	stomach
24	chr8:6420800-6424000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr8:6420800-6424200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr8:6420800-6424400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr8:6420800-6427600	Weak transcription	NHDF-Ad	bronchial
28	chr8:6420800-6429800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr8:6420800-6433200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr8:6421000-6421400	Enhancers	Colon Smooth Muscle	Colon
31	chr8:6421000-6421600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr8:6421000-6421800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr8:6421000-6422000	Weak transcription	Placenta	Placenta
34	chr8:6421000-6422200	Weak transcription	Fetal Intestine Small	intestine
35	chr8:6421000-6423000	Weak transcription	Brain Hippocampus Middle	brain
36	chr8:6421000-6423800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr8:6421000-6423800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr8:6421000-6423800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr8:6421000-6423800	Weak transcription	Esophagus	oesophagus
40	chr8:6421000-6423800	Weak transcription	Lung	lung
41	chr8:6421000-6423800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr8:6421000-6424600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr8:6421000-6424800	Weak transcription	Fetal Thymus	thymus
44	chr8:6421000-6425200	Weak transcription	Fetal Muscle Leg	muscle
45	chr8:6421000-6425400	Weak transcription	Fetal Stomach	stomach
46	chr8:6421000-6425800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr8:6421000-6426000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr8:6421000-6427400	Weak transcription	Left Ventricle	heart
49	chr8:6421000-6427400	Weak transcription	Ovary	ovary
50	chr8:6421000-6427800	Weak transcription	Aorta	Aorta

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