Variant report

Variant	rs16864258
Chromosome Location	chr1:171226034-171226035
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10912675	0.83[JPT][hapmap]
rs10912698	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10912718	0.82[AFR][1000 genomes]
rs10912745	0.82[AFR][1000 genomes]
rs10912756	0.80[AFR][1000 genomes]
rs12022278	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12022340	0.85[AMR][1000 genomes]
rs12040753	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12044884	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12118836	0.82[AFR][1000 genomes]
rs12124080	0.81[AFR][1000 genomes]
rs12127128	0.82[AFR][1000 genomes]
rs12954	0.84[ASW][hapmap];0.83[LWK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs2076320	1.00[ASW][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs2421804	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3766654	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs72714180	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs732005	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16864258	PRDX6	cis	parietal	SCAN
rs16864258	FMO1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171221000-171226600	Weak transcription	Esophagus	oesophagus
2	chr1:171221000-171227600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:171221200-171226400	Weak transcription	Right Atrium	heart
4	chr1:171221200-171227200	Enhancers	Fetal Intestine Small	intestine
5	chr1:171221200-171228200	Enhancers	Fetal Intestine Large	intestine
6	chr1:171221400-171226200	Weak transcription	Fetal Heart	heart
7	chr1:171221800-171226400	Weak transcription	Pancreas	Pancrea
8	chr1:171221800-171226800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:171221800-171226800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:171222000-171226200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:171222000-171226400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:171222000-171226600	Weak transcription	Placenta	Placenta
13	chr1:171222000-171227200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:171222000-171227400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:171224400-171227200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:171224600-171226400	Weak transcription	Gastric	stomach
17	chr1:171224800-171226600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:171224800-171227400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:171224800-171227800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:171225000-171226200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:171225000-171226400	Weak transcription	Small Intestine	intestine
22	chr1:171225000-171226400	Weak transcription	NHDF-Ad	bronchial
23	chr1:171225000-171227200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:171225000-171227600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:171225000-171228000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:171225600-171227200	Enhancers	Fetal Muscle Leg	muscle
27	chr1:171225800-171226200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:171226000-171226800	Enhancers	Liver	Liver
29	chr1:171226000-171226800	Enhancers	Fetal Kidney	kidney
30	chr1:171226000-171226800	Enhancers	Fetal Lung	lung
31	chr1:171226000-171226800	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr1:171226000-171227200	Enhancers	HMEC	breast
33	chr1:171226000-171227400	Enhancers	Duodenum Mucosa	Duodenum
34	chr1:171226000-171228000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:171226000-171228600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:171226000-171228800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:171226000-171228800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:171226000-171228800	Enhancers	NHEK	skin
39	chr1:171226000-171229200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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