Variant report

Variant	rs2461837
Chromosome Location	chr17:18265467-18265468
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18149918..18152295-chr17:18264840..18266898,2	MCF-7	breast:
2	chr17:18253996..18255847-chr17:18263944..18265706,2	MCF-7	breast:
3	chr17:18137212..18138850-chr17:18263977..18266031,2	K562	blood:
4	chr17:18217812..18219938-chr17:18264805..18267202,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177731	Chromatin interaction
ENSG00000177302	Chromatin interaction
ENSG00000131899	Chromatin interaction
ENSG00000176994	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11870126	0.80[AMR][1000 genomes]
rs12936652	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs12936769	0.80[AMR][1000 genomes]
rs12937300	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12939092	0.93[EUR][1000 genomes]
rs12939757	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes]
rs12945597	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs12952556	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs12952667	0.81[EUR][1000 genomes]
rs1563631	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1979276	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1979277	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs2230154	0.82[AMR][1000 genomes]
rs2273028	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs2273030	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs2386456	0.82[AMR][1000 genomes]
rs2461838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605142	1.00[CHB][hapmap]
rs2746023	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs2746025	0.83[YRI][hapmap]
rs3783	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3794772	0.83[EUR][1000 genomes]
rs3829583	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs4632181	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4924750	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4924845	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs4924847	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs4924849	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4925160	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs4925171	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs4925172	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs643333	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502644	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs6502646	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6502649	0.82[EUR][1000 genomes]
rs672356	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7207123	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs7207306	0.84[CEU][hapmap];0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7215839	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs7222684	0.81[EUR][1000 genomes]
rs8070633	0.82[EUR][1000 genomes]
rs8071231	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs8073464	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8080966	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs921865	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs921866	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs921986	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs941451	0.92[CEU][hapmap];1.00[CHB][hapmap]

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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	esv2758443	chr17:18234525-18446384	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
10	esv2758677	chr17:18234525-18446384	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
11	esv1829832	chr17:18235992-18405148	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
12	nsv827913	chr17:18253785-18572122	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv1065708	chr17:18259174-18913343	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2461837	SHMT1	cis	Artery Tibial	GTEx
rs2461837	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs2461837	LLGL1	cis	Esophagus Mucosa	GTEx
rs2461837	SHMT1	cis	Nerve Tibial	GTEx
rs2461837	LGALS9C	cis	Whole Blood	GTEx
rs2461837	SHMT1	cis	multi-tissue	Pritchard
rs2461837	SHMT1	cis	Muscle Skeletal	GTEx
rs2461837	SHMT1	cis	Esophagus Muscularis	GTEx
rs2461837	SHMT1	cis	Artery Aorta	GTEx
rs2461837	SHMT1	cis	Whole Blood	GTEx
rs2461837	RP11-258F1.1	cis	Esophagus Muscularis	GTEx
rs2461837	SHMT1	cis	Frontal Cortex	GTEx
rs2461837	ALKBH5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18219400-18266000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18222400-18266200	Weak transcription	Small Intestine	intestine
3	chr17:18228200-18265800	Weak transcription	Fetal Brain Male	brain
4	chr17:18228600-18266000	Weak transcription	HSMM	muscle
5	chr17:18229000-18266000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr17:18230200-18265600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr17:18231000-18266000	Weak transcription	Psoas Muscle	Psoas
8	chr17:18244400-18266200	Weak transcription	Stomach Mucosa	stomach
9	chr17:18245400-18266000	Weak transcription	NH-A	brain
10	chr17:18250200-18265800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr17:18251800-18266000	Weak transcription	Right Ventricle	heart
12	chr17:18252000-18265800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr17:18252000-18266000	Weak transcription	NHLF	lung
14	chr17:18252200-18265800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr17:18252200-18266000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:18252200-18266000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr17:18252400-18265800	Weak transcription	HUVEC	blood vessel
18	chr17:18256200-18266000	Weak transcription	Aorta	Aorta
19	chr17:18256800-18266000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr17:18256800-18266000	Weak transcription	Colonic Mucosa	Colon
21	chr17:18257000-18265800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr17:18257000-18265800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr17:18257000-18265800	Weak transcription	Primary B cells from cord blood	blood
24	chr17:18257000-18265800	Weak transcription	Esophagus	oesophagus
25	chr17:18257000-18265800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr17:18257000-18266000	Weak transcription	Gastric	stomach
27	chr17:18257000-18266000	Weak transcription	Left Ventricle	heart
28	chr17:18257000-18266000	Weak transcription	Ovary	ovary
29	chr17:18257400-18265800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr17:18257400-18266000	Weak transcription	Colon Smooth Muscle	Colon
31	chr17:18257400-18266000	Weak transcription	Fetal Lung	lung
32	chr17:18257400-18266000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr17:18258000-18265800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr17:18258000-18265800	Weak transcription	Placenta	Placenta
35	chr17:18258400-18266000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr17:18260000-18265800	Weak transcription	Lung	lung
37	chr17:18260400-18266000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr17:18260800-18265600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr17:18260800-18266000	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr17:18261000-18266000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr17:18261000-18266000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr17:18261200-18265600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr17:18262400-18265600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr17:18263800-18266000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr17:18263800-18266000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr17:18263800-18266000	Weak transcription	Fetal Intestine Small	intestine
47	chr17:18264000-18266000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr17:18264200-18266000	Weak transcription	Fetal Intestine Large	intestine
49	chr17:18264200-18266800	Active TSS	Liver	Liver
50	chr17:18264600-18265800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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