Variant report

Variant	rs3829583
Chromosome Location	chr17:18216745-18216746
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18204042..18206073-chr17:18215565..18218215,2	MCF-7	breast:
2	chr17:18207672..18211933-chr17:18214098..18218432,6	MCF-7	breast:
3	chr17:18185665..18188160-chr17:18215584..18219242,3	MCF-7	breast:
4	chr17:18159194..18166260-chr17:18215929..18222740,16	MCF-7	breast:
5	chr17:18156705..18166530-chr17:18215131..18220177,19	MCF-7	breast:
6	chr17:18127269..18131326-chr17:18216439..18220320,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177302	Chromatin interaction
ENSG00000177427	Chromatin interaction
ENSG00000177731	Chromatin interaction
ENSG00000131899	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11868259	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11870126	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12936652	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12936769	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12937300	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12939092	0.80[EUR][1000 genomes]
rs12939259	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939357	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939757	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12945597	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12946058	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12949078	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949983	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12952556	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12952667	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1563631	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1563633	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979277	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2230154	1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2273030	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386456	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2386457	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2386458	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2461837	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs2461838	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs2605142	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746023	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746024	0.97[ASN][1000 genomes]
rs28419113	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764405	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3783	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3794771	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794772	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4632181	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924750	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4924842	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924843	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4924845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924847	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924849	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4925160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925162	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925163	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925167	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925169	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925171	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58215032	0.88[EUR][1000 genomes]
rs643333	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs6502643	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502644	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502646	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502649	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66903818	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207306	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7215839	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7222684	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7223122	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068602	0.86[EUR][1000 genomes]
rs8068854	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070633	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8071231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073464	0.81[EUR][1000 genomes]
rs8074444	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8080966	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921866	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs941451	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9898631	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv833387	chr17:18200081-18378155	Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS 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	34 gene(s)	inside rSNPs	diseases
10	esv1806346	chr17:18200081-18446384	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	esv1812661	chr17:18200081-18446384	Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv428333	chr17:18200081-18446384	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
13	nsv427992	chr17:18200081-19192047	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3829583	SHMT1	cis	Muscle Skeletal	GTEx
rs3829583	LLGL1	cis	Esophagus Mucosa	GTEx
rs3829583	SHMT1	cis	Artery Tibial	GTEx
rs3829583	SHMT1	cis	multi-tissue	Pritchard
rs3829583	SHMT1	cis	Nerve Tibial	GTEx
rs3829583	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs3829583	SHMT1	cis	Esophagus Muscularis	GTEx
rs3829583	ALKBH5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 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	chr17:18184800-18217000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:18196800-18217000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr17:18203200-18216800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr17:18206800-18217000	Weak transcription	Stomach Mucosa	stomach
6	chr17:18208800-18217000	Weak transcription	Right Ventricle	heart
7	chr17:18210200-18217000	Weak transcription	Psoas Muscle	Psoas
8	chr17:18210600-18217200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:18211200-18216800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr17:18211200-18217000	Weak transcription	Ovary	ovary
11	chr17:18211200-18217200	Weak transcription	Aorta	Aorta
12	chr17:18215200-18216800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr17:18215200-18217000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
14	chr17:18215400-18216800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr17:18215400-18217000	Genic enhancers	Fetal Muscle Leg	muscle
16	chr17:18215400-18217000	Enhancers	Gastric	stomach
17	chr17:18215400-18217200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr17:18215400-18217200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr17:18215400-18217400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr17:18215400-18217400	Transcr. at gene 5' and 3'	Dnd41	blood
21	chr17:18215600-18216800	Genic enhancers	Brain Cingulate Gyrus	brain
22	chr17:18215600-18217000	Enhancers	Brain Angular Gyrus	brain
23	chr17:18215600-18217000	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr17:18215600-18217200	Enhancers	Colon Smooth Muscle	Colon
25	chr17:18215600-18217200	Enhancers	Fetal Heart	heart
26	chr17:18215800-18216800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr17:18215800-18217000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr17:18215800-18217000	Weak transcription	Colonic Mucosa	Colon
29	chr17:18215800-18217000	Weak transcription	Left Ventricle	heart
30	chr17:18215800-18217000	Weak transcription	Lung	lung
31	chr17:18215800-18217000	Weak transcription	Right Atrium	heart
32	chr17:18215800-18217000	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr17:18216000-18216800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr17:18216000-18216800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr17:18216000-18216800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr17:18216000-18216800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr17:18216000-18216800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr17:18216000-18216800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr17:18216000-18217000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr17:18216000-18217000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr17:18216000-18217000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr17:18216000-18217000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr17:18216000-18217000	Active TSS	Fetal Brain Female	brain
44	chr17:18216000-18217000	Enhancers	Fetal Kidney	kidney
45	chr17:18216000-18217000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr17:18216000-18217200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr17:18216000-18217200	Enhancers	Primary T cells fromperipheralblood	blood
48	chr17:18216000-18217400	Flanking Active TSS	GM12878-XiMat	blood
49	chr17:18216200-18216800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr17:18216200-18216800	Weak transcription	H9 Cell Line	embryonic stem cell

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