Variant report

Variant	rs2461838
Chromosome Location	chr17:18265264-18265265
allele	C/T
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
ENSG00000131899	Chromatin interaction
ENSG00000176994	Chromatin interaction
ENSG00000177302	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11870126	0.80[AMR][1000 genomes]
rs12936652	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs12936694	0.90[CHD][hapmap]
rs12936769	0.80[AMR][1000 genomes]
rs12937300	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12939092	0.92[EUR][1000 genomes]
rs12939469	0.90[CHD][hapmap]
rs12939757	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes]
rs12945597	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap]
rs12952556	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.80[EUR][1000 genomes]
rs12952667	0.80[EUR][1000 genomes]
rs1378601	0.90[CHD][hapmap]
rs1378602	0.90[CHD][hapmap]
rs1563631	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1979276	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap]
rs1979277	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs2230154	0.82[AMR][1000 genomes]
rs2273028	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes]
rs2273030	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs2360234	0.90[CHD][hapmap]
rs2386456	0.82[AMR][1000 genomes]
rs2461837	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]
rs2605136	0.90[CHD][hapmap]
rs2605142	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs2746023	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2746025	1.00[CHD][hapmap];0.83[YRI][hapmap]
rs2746027	1.00[CHD][hapmap]
rs3783	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[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]
rs4603612	0.82[CHD][hapmap]
rs4632181	0.82[AMR][1000 genomes]
rs4924750	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4924839	0.90[CHD][hapmap]
rs4924841	0.90[CHD][hapmap]
rs4924845	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs4924847	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs4924849	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4925160	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs4925171	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.80[EUR][1000 genomes]
rs4925172	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs643333	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502644	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs6502646	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[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];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7207123	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[MEX][hapmap]
rs7207306	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7215839	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap]
rs7222684	0.80[EUR][1000 genomes]
rs8070633	0.81[EUR][1000 genomes]
rs8071231	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs8071834	0.90[CHD][hapmap]
rs8073464	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8080966	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes]
rs854795	0.90[CHD][hapmap]
rs854804	0.90[CHD][hapmap]
rs860568	0.90[CHD][hapmap]
rs921865	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs921866	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs921986	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap]
rs941451	0.91[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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs2461838	MAPK7	cis	cerebellum	SCAN
rs2461838	TOP3A	cis	cerebellum	SCAN
rs2461838	SHMT1	cis	Frontal Cortex	GTEx
rs2461838	SHMT1	cis	Whole Blood	GTEx
rs2461838	RP11-258F1.1	cis	Esophagus Muscularis	GTEx
rs2461838	MYO15A	cis	cerebellum	SCAN
rs2461838	ALKBH5	cis	Esophagus Muscularis	GTEx
rs2461838	SHMT1	cis	Muscle Skeletal	GTEx
rs2461838	SHMT1	cis	lymphoblastoid	seeQTL
rs2461838	SHMT1	cis	Artery Aorta	GTEx
rs2461838	LOC162632	cis	parietal	SCAN
rs2461838	LGALS9C	cis	Whole Blood	GTEx
rs2461838	SHMT1	cis	Esophagus Muscularis	GTEx
rs2461838	SHMT1	cis	Nerve Tibial	GTEx
rs2461838	SHMT1	cis	Artery Tibial	GTEx
rs2461838	PIGL	cis	parietal	SCAN
rs2461838	LOC162632	cis	cerebellum	SCAN
rs2461838	SHMT1	cis	multi-tissue	Pritchard
rs2461838	LLGL1	cis	Esophagus Mucosa	GTEx
rs2461838	FLJ36492	cis	multi-tissue	Pritchard

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	chr17:18223600-18265400	Strong transcription	Fetal Stomach	stomach
4	chr17:18228200-18265800	Weak transcription	Fetal Brain Male	brain
5	chr17:18228600-18266000	Weak transcription	HSMM	muscle
6	chr17:18229000-18266000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:18230200-18265600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:18231000-18266000	Weak transcription	Psoas Muscle	Psoas
9	chr17:18235800-18265400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr17:18244400-18266200	Weak transcription	Stomach Mucosa	stomach
11	chr17:18245400-18266000	Weak transcription	NH-A	brain
12	chr17:18250200-18265400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:18250200-18265800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr17:18251800-18266000	Weak transcription	Right Ventricle	heart
15	chr17:18252000-18265800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr17:18252000-18266000	Weak transcription	NHLF	lung
17	chr17:18252200-18265800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr17:18252200-18266000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:18252200-18266000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr17:18252400-18265800	Weak transcription	HUVEC	blood vessel
21	chr17:18256200-18266000	Weak transcription	Aorta	Aorta
22	chr17:18256800-18266000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr17:18256800-18266000	Weak transcription	Colonic Mucosa	Colon
24	chr17:18257000-18265400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr17:18257000-18265400	Weak transcription	Brain Germinal Matrix	brain
26	chr17:18257000-18265400	Weak transcription	Fetal Brain Female	brain
27	chr17:18257000-18265800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr17:18257000-18265800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr17:18257000-18265800	Weak transcription	Primary B cells from cord blood	blood
30	chr17:18257000-18265800	Weak transcription	Esophagus	oesophagus
31	chr17:18257000-18265800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr17:18257000-18266000	Weak transcription	Gastric	stomach
33	chr17:18257000-18266000	Weak transcription	Left Ventricle	heart
34	chr17:18257000-18266000	Weak transcription	Ovary	ovary
35	chr17:18257200-18265400	Weak transcription	Primary T cells from cord blood	blood
36	chr17:18257400-18265400	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr17:18257400-18265400	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr17:18257400-18265800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr17:18257400-18266000	Weak transcription	Colon Smooth Muscle	Colon
40	chr17:18257400-18266000	Weak transcription	Fetal Lung	lung
41	chr17:18257400-18266000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr17:18257800-18265400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr17:18258000-18265400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr17:18258000-18265800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr17:18258000-18265800	Weak transcription	Placenta	Placenta
46	chr17:18258400-18266000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr17:18260000-18265800	Weak transcription	Lung	lung
48	chr17:18260400-18266000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr17:18260800-18265600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr17:18260800-18266000	Weak transcription	Monocytes-CD14+_RO01746	blood

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