Variant report

Variant	rs66903818
Chromosome Location	chr17:18199388-18199389
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18162298..18165482-chr17:18198310..18200966,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177427	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11868259	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11870126	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12936652	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12936769	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12937300	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12939092	0.82[EUR][1000 genomes]
rs12939259	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939357	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939757	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12945597	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12946058	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12949078	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949983	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12952556	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12952667	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1563631	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1563633	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979276	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979277	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2230154	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273028	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2273030	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386456	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2386457	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2386458	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605142	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746023	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746024	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28419113	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764405	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3783	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3794771	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794772	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3829583	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4632181	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924750	0.81[EUR][1000 genomes]
rs4924842	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924843	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4924845	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924847	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924849	0.83[EUR][1000 genomes]
rs4925160	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925162	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925163	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925167	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925169	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925171	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925172	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58215032	0.90[EUR][1000 genomes]
rs6502643	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502644	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502646	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502649	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7207123	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215839	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7222684	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7223122	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068602	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8068854	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070633	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8071231	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073464	0.83[EUR][1000 genomes]
rs8074444	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8080966	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921865	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921866	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921986	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs941451	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9898631	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription 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	47 gene(s)	inside rSNPs	diseases
5	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers 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	21 gene(s)	inside rSNPs	diseases
7	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv907775	chr17:18108496-18206234	Strong transcription Weak transcription Flanking Active TSS Enhancers 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	21 gene(s)	inside rSNPs	diseases
9	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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 miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv1057081	chr17:18171516-18256347	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv543247	chr17:18171516-18256347	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	nsv1062368	chr17:18180747-18259234	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs66903818	SHMT1	cis	Esophagus Muscularis	GTEx
rs66903818	LGALS9C	cis	Whole Blood	GTEx
rs66903818	SHMT1	cis	Muscle Skeletal	GTEx
rs66903818	LLGL1	cis	Esophagus Mucosa	GTEx
rs66903818	SHMT1	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18172200-18217400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18172400-18201000	Strong transcription	Fetal Stomach	stomach
3	chr17:18173000-18200400	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr17:18173000-18213800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:18173200-18200200	Strong transcription	Placenta	Placenta
6	chr17:18173400-18200200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr17:18173400-18200800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:18173400-18201000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr17:18173400-18201000	Strong transcription	Fetal Intestine Small	intestine
10	chr17:18173600-18200200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr17:18173600-18200800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr17:18174000-18200600	Strong transcription	Dnd41	blood
13	chr17:18174200-18200600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr17:18174800-18200600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr17:18175600-18200800	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr17:18175800-18200800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:18175800-18201000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr17:18176200-18200800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr17:18176400-18200200	Strong transcription	Fetal Intestine Large	intestine
20	chr17:18176400-18200200	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr17:18176400-18201000	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr17:18176600-18200200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr17:18176600-18200800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr17:18181200-18200800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr17:18181400-18200200	Strong transcription	Fetal Muscle Leg	muscle
26	chr17:18183000-18200800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr17:18183400-18200800	Strong transcription	Fetal Brain Female	brain
28	chr17:18183600-18207000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr17:18184600-18201000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr17:18184800-18217000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr17:18185200-18200000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr17:18185200-18200200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr17:18189000-18202800	Weak transcription	Stomach Mucosa	stomach
34	chr17:18190200-18200200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr17:18191600-18200200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr17:18192000-18200200	Strong transcription	Brain Anterior Caudate	brain
37	chr17:18193000-18200200	Strong transcription	Hela-S3	cervix
38	chr17:18193800-18204000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr17:18194400-18202800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr17:18194600-18202600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr17:18194600-18202600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr17:18194600-18208000	Weak transcription	Fetal Brain Male	brain
43	chr17:18194600-18215600	Weak transcription	Fetal Heart	heart
44	chr17:18195800-18209600	Weak transcription	Psoas Muscle	Psoas
45	chr17:18196000-18202600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr17:18196000-18204200	Weak transcription	Small Intestine	intestine
47	chr17:18196200-18202600	Weak transcription	Colon Smooth Muscle	Colon
48	chr17:18196400-18202600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr17:18196400-18202600	Weak transcription	Pancreas	Pancrea
50	chr17:18196600-18199600	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links