Variant report

Variant	rs669340
Chromosome Location	chr17:18263957-18263958
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18253996..18255847-chr17:18263944..18265706,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12946752	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs12950117	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1563632	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs1563634	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs1682280	0.89[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs2071241	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs2273027	0.82[JPT][hapmap]
rs2461847	0.84[GIH][hapmap];0.89[TSI][hapmap]
rs2605141	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs2605144	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs2688030	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2688036	0.89[ASN][1000 genomes]
rs2688052	0.81[EUR][1000 genomes]
rs28597812	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4398149	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4924846	0.83[ASN][1000 genomes]
rs4925166	0.81[ASN][1000 genomes]
rs4925179	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs584300	0.84[GIH][hapmap];0.89[TSI][hapmap]
rs593297	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs638318	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs638416	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs641028	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs651234	0.92[ASN][1000 genomes]
rs652093	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7212104	0.82[ASN][1000 genomes]
rs7222009	0.84[GIH][hapmap];0.89[TSI][hapmap]
rs7225932	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs8065874	0.86[JPT][hapmap]
rs8080936	0.83[EUR][1000 genomes]
rs8080951	0.82[JPT][hapmap]
rs921985	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv978377	chr17:18251618-18265255	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	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
14	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:23)

SNP	Gene	Cis/trans	Tissue	Source
rs669340	SHMT1	cis	multi-tissue	Pritchard
rs669340	SHMT1	cis	Muscle Skeletal	GTEx
rs669340	LGALS9C	cis	Whole Blood	GTEx
rs669340	USP32P2	cis	Artery Tibial	GTEx
rs669340	SHMT1	cis	parietal	SCAN
rs669340	FAM106A	cis	lung	GTEx
rs669340	USP32P2	cis	lung	GTEx
rs669340	SHMT1	cis	Esophagus Muscularis	GTEx
rs669340	FAM106A	cis	Thyroid	GTEx
rs669340	USP32P2	cis	Thyroid	GTEx
rs669340	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs669340	TOP3A	cis	cerebellum	SCAN
rs669340	SHMT1	cis	Artery Aorta	GTEx
rs669340	FLJ36492	cis	multi-tissue	Pritchard
rs669340	SHMT1	cis	Artery Tibial	GTEx
rs669340	SHMT1	cis	lymphoblastoid	seeQTL
rs669340	LOC162632	cis	parietal	SCAN
rs669340	LOC162632	cis	cerebellum	SCAN
rs669340	USP32P2	cis	Esophagus Mucosa	GTEx
rs669340	USP32P2	cis	Whole Blood	GTEx
rs669340	SHMT1	cis	Nerve Tibial	GTEx
rs669340	SHMT1	cis	Whole Blood	GTEx
rs669340	USP32P2	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 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	chr17:18242400-18264000	Strong transcription	Fetal Thymus	thymus
11	chr17:18243800-18264200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr17:18244400-18264200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:18244400-18264200	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr17:18244400-18266200	Weak transcription	Stomach Mucosa	stomach
15	chr17:18245400-18266000	Weak transcription	NH-A	brain
16	chr17:18250200-18265200	Weak transcription	Fetal Kidney	kidney
17	chr17:18250200-18265200	Weak transcription	K562	blood
18	chr17:18250200-18265400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr17:18250200-18265800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr17:18251000-18265200	Weak transcription	Pancreas	Pancrea
21	chr17:18251000-18265200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr17:18251800-18266000	Weak transcription	Right Ventricle	heart
23	chr17:18252000-18265200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr17:18252000-18265800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr17:18252000-18266000	Weak transcription	NHLF	lung
26	chr17:18252200-18265800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr17:18252200-18266000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:18252200-18266000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr17:18252400-18265800	Weak transcription	HUVEC	blood vessel
30	chr17:18255600-18265200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr17:18256200-18266000	Weak transcription	Aorta	Aorta
32	chr17:18256800-18265200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr17:18256800-18266000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr17:18256800-18266000	Weak transcription	Colonic Mucosa	Colon
35	chr17:18257000-18265000	Weak transcription	Brain Angular Gyrus	brain
36	chr17:18257000-18265200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr17:18257000-18265200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr17:18257000-18265200	Weak transcription	Brain Substantia Nigra	brain
39	chr17:18257000-18265200	Weak transcription	Spleen	Spleen
40	chr17:18257000-18265400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr17:18257000-18265400	Weak transcription	Brain Germinal Matrix	brain
42	chr17:18257000-18265400	Weak transcription	Fetal Brain Female	brain
43	chr17:18257000-18265800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr17:18257000-18265800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr17:18257000-18265800	Weak transcription	Primary B cells from cord blood	blood
46	chr17:18257000-18265800	Weak transcription	Esophagus	oesophagus
47	chr17:18257000-18265800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr17:18257000-18266000	Weak transcription	Gastric	stomach
49	chr17:18257000-18266000	Weak transcription	Left Ventricle	heart
50	chr17:18257000-18266000	Weak transcription	Ovary	ovary

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