Variant report

Variant	rs7200258
Chromosome Location	chr16:69897469-69897470
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:69896893..69899851-chr16:69904194..69906022,2	K562	blood:

Variant related genes	Relation type
ENSG00000198373	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10852460	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10852461	0.88[ASN][1000 genomes]
rs11075742	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11075744	0.90[ASN][1000 genomes]
rs1116544	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11642008	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11648348	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12927168	0.82[EUR][1000 genomes]
rs1466863	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1500337	0.92[ASN][1000 genomes]
rs1566453	0.88[ASN][1000 genomes]
rs1566454	0.92[ASN][1000 genomes]
rs1566456	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2133799	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2362642	0.88[ASN][1000 genomes]
rs3790075	0.92[ASN][1000 genomes]
rs3790076	0.92[ASN][1000 genomes]
rs3790080	0.92[ASN][1000 genomes]
rs3790082	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3790083	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985447	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4985448	0.92[ASN][1000 genomes]
rs4985449	0.92[ASN][1000 genomes]
rs4985450	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55887947	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6499263	0.90[ASN][1000 genomes]
rs6499265	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6499268	0.92[ASN][1000 genomes]
rs6499269	0.81[ASN][1000 genomes]
rs7190013	0.92[ASN][1000 genomes]
rs7202233	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8047194	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8047682	0.88[ASN][1000 genomes]
rs8048550	0.92[ASN][1000 genomes]
rs8049373	0.88[ASN][1000 genomes]
rs8050414	0.83[ASN][1000 genomes]
rs8050516	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8051168	0.88[ASN][1000 genomes]
rs8060478	0.88[ASN][1000 genomes]
rs8063226	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9927967	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9936589	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9936723	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1062171	chr16:69854267-70188585	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv542941	chr16:69854267-70188585	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1059249	chr16:69854467-70188446	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv542942	chr16:69854467-70188446	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers 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 miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2758428	chr16:69855122-70313222	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2758652	chr16:69855122-70313222	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7200258	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69834000-69910600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr16:69837000-69905600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr16:69874000-69905800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr16:69876000-69904400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr16:69876000-69905800	Weak transcription	Dnd41	blood
6	chr16:69876200-69905800	Weak transcription	Brain Germinal Matrix	brain
7	chr16:69883000-69899400	Weak transcription	NHLF	lung
8	chr16:69883400-69899600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr16:69883400-69903800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:69883600-69904400	Weak transcription	HMEC	breast
11	chr16:69887600-69901400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr16:69888000-69901400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr16:69888000-69905600	Weak transcription	Gastric	stomach
14	chr16:69889200-69899800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr16:69889600-69905600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr16:69890400-69923400	Weak transcription	HUVEC	blood vessel
17	chr16:69891000-69898600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr16:69891200-69898400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr16:69891600-69898600	Enhancers	Pancreas	Pancrea
20	chr16:69892600-69905400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr16:69893000-69906800	Weak transcription	GM12878-XiMat	blood
22	chr16:69893000-69907000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr16:69893000-69934800	Weak transcription	Hela-S3	cervix
24	chr16:69893200-69898000	Enhancers	HepG2	liver
25	chr16:69893200-69899600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr16:69893200-69901000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr16:69893200-69901000	Weak transcription	Fetal Thymus	thymus
28	chr16:69893200-69901200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr16:69893200-69901400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr16:69893200-69903800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr16:69893200-69904600	Weak transcription	NHEK	skin
32	chr16:69893200-69906400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr16:69893200-69923000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr16:69893400-69899400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr16:69893400-69901200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr16:69893400-69905000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr16:69893400-69906400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr16:69893600-69899000	Weak transcription	K562	blood
39	chr16:69893600-69905600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr16:69893600-69910600	Weak transcription	A549	lung
41	chr16:69894200-69899600	Weak transcription	Placenta	Placenta
42	chr16:69894200-69903800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr16:69894600-69901000	Weak transcription	Thymus	Thymus
44	chr16:69895200-69901000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr16:69895200-69901000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr16:69895200-69901200	Weak transcription	Esophagus	oesophagus
47	chr16:69895200-69901200	Weak transcription	Spleen	Spleen
48	chr16:69895200-69905600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr16:69895400-69899600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr16:69895400-69901000	Weak transcription	Fetal Intestine Large	intestine

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