Variant report

Variant	rs16864245
Chromosome Location	chr1:171222380-171222381
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12064117	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12066662	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12071595	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12072321	0.84[AMR][1000 genomes]
rs12082112	0.84[AMR][1000 genomes]
rs12087971	1.00[CEU][hapmap]
rs12091865	1.00[CEU][hapmap]
rs13353034	0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16864165	1.00[CEU][hapmap]
rs16864191	1.00[CEU][hapmap]
rs17350523	0.85[YRI][hapmap]
rs2020860	1.00[CEU][hapmap]
rs2020865	1.00[CEU][hapmap]
rs2205726	0.84[AMR][1000 genomes]
rs56060753	0.84[AMR][1000 genomes]
rs56159716	0.84[AMR][1000 genomes]
rs56233063	0.84[AMR][1000 genomes]
rs58956470	0.84[AMR][1000 genomes]
rs59910498	0.84[AMR][1000 genomes]
rs61225278	0.80[EUR][1000 genomes]
rs61233777	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6668231	1.00[CEU][hapmap]
rs6684218	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6689616	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs74122287	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7527107	0.89[AMR][1000 genomes];0.89[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16864245	FMO2	cis	brain	BrainEAC

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171221000-171222600	Enhancers	Dnd41	blood
2	chr1:171221000-171223800	Weak transcription	HMEC	breast
3	chr1:171221000-171224400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:171221000-171226000	Weak transcription	Fetal Kidney	kidney
5	chr1:171221000-171226600	Weak transcription	Esophagus	oesophagus
6	chr1:171221000-171227600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:171221200-171223600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:171221200-171223600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:171221200-171223600	Weak transcription	Osteobl	bone
10	chr1:171221200-171223800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:171221200-171224400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:171221200-171224400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:171221200-171224600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:171221200-171226000	Weak transcription	Liver	Liver
15	chr1:171221200-171226000	Weak transcription	Fetal Lung	lung
16	chr1:171221200-171226400	Weak transcription	Right Atrium	heart
17	chr1:171221200-171227200	Enhancers	Fetal Intestine Small	intestine
18	chr1:171221200-171228200	Enhancers	Fetal Intestine Large	intestine
19	chr1:171221400-171223800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:171221400-171223800	Weak transcription	NH-A	brain
21	chr1:171221400-171226200	Weak transcription	Fetal Heart	heart
22	chr1:171221800-171222600	Enhancers	GM12878-XiMat	blood
23	chr1:171221800-171222800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr1:171221800-171223600	Weak transcription	NHEK	skin
25	chr1:171221800-171226400	Weak transcription	Pancreas	Pancrea
26	chr1:171221800-171226800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:171221800-171226800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:171222000-171223600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:171222000-171223800	Weak transcription	Gastric	stomach
30	chr1:171222000-171224400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:171222000-171226200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:171222000-171226400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:171222000-171226600	Weak transcription	Placenta	Placenta
34	chr1:171222000-171227200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:171222000-171227400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:171222200-171224400	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links