Variant report

Variant	rs6488089
Chromosome Location	chr12:32942278-32942279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1046150	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743802	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771995	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772000	0.94[ASN][1000 genomes]
rs10772004	0.81[CHB][hapmap]
rs10844349	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11052246	0.94[ASN][1000 genomes]
rs12612	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35960561	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6488084	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6488086	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6488088	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488091	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488092	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488093	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7298089	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7304383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312621	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956824	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957460	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394	0.94[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv530421	chr12:32825335-33465991	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1054440	chr12:32872999-33150460	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv532334	chr12:32884789-33034791	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv1851844	chr12:32929596-32953032	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32933200-32944800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:32934000-32944000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:32934200-32945200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:32936200-32948800	Weak transcription	Fetal Stomach	stomach
5	chr12:32936400-32947000	Weak transcription	Fetal Heart	heart
6	chr12:32937400-32945400	Weak transcription	NHEK	skin
7	chr12:32938600-32948600	Weak transcription	Gastric	stomach
8	chr12:32938600-32952200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:32938800-32945000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:32938800-32950600	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:32939000-32944800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:32939200-32955200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:32939400-32945200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:32939600-32944800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:32939600-32945000	Weak transcription	Fetal Intestine Large	intestine
16	chr12:32939800-32943200	Weak transcription	HMEC	breast
17	chr12:32940400-32942400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:32940400-32942400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:32940600-32946600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:32940800-32961800	Weak transcription	Colonic Mucosa	Colon
21	chr12:32941000-32944400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:32941200-32944400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:32941200-32949200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:32941600-32942400	Strong transcription	Fetal Intestine Small	intestine
25	chr12:32941600-32943200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:32941800-32944800	Weak transcription	Placenta	Placenta
27	chr12:32941800-32945000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:32941800-32948800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr12:32941800-33033400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:32942000-32949400	Strong transcription	Liver	Liver
31	chr12:32942000-32957400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:32942200-32943000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr12:32942200-32943600	Strong transcription	Left Ventricle	heart
34	chr12:32942200-32950600	Weak transcription	Ovary	ovary

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