Variant report

Variant	rs7225932
Chromosome Location	chr17:18208334-18208335
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:18208296-18208641	HepG2	liver:	n/a	n/a
2	POLR2A	chr17:18208290-18208538	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:18207048..18208601-chr17:18217064..18219249,2	K562	blood:
2	chr17:18162871..18165268-chr17:18208056..18210567,2	MCF-7	breast:
3	chr17:18207672..18211933-chr17:18214098..18218432,6	MCF-7	breast:

Variant related genes	Relation type
TOP3A	TF binding region
ENSG00000228000	Chromatin interaction
ENSG00000176994	Chromatin interaction
ENSG00000237382	Chromatin interaction
ENSG00000177302	Chromatin interaction
ENSG00000177427	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12946752	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12950117	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1563632	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1563634	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1682280	0.80[LWK][hapmap];0.83[TSI][hapmap]
rs2071241	0.82[ASW][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2245430	0.93[GIH][hapmap]
rs2273027	0.87[JPT][hapmap]
rs2473656	0.93[GIH][hapmap]
rs2605141	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2605143	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2605144	0.82[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2605145	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2688030	0.81[EUR][1000 genomes]
rs3764404	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924846	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4925144	0.87[GIH][hapmap]
rs4925166	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925179	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs641028	0.81[AMR][1000 genomes]
rs6502647	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6502650	0.83[AMR][1000 genomes]
rs669340	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs712274	0.86[GIH][hapmap]
rs7212104	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8065874	0.82[JPT][hapmap]
rs8076253	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs854800	0.84[GIH][hapmap]
rs854802	0.84[GIH][hapmap]
rs854803	0.84[GIH][hapmap]
rs921985	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs7225932	SHMT1	cis	Muscle Skeletal	GTEx
rs7225932	SHMT1	cis	Whole Blood	GTEx
rs7225932	FAM106A	cis	Thyroid	GTEx
rs7225932	LOC162632	cis	cerebellum	SCAN
rs7225932	SHMT1	cis	multi-tissue	Pritchard
rs7225932	SHMT1	cis	Artery Tibial	GTEx
rs7225932	SHMT1	cis	Lymphoblastoid	GTEx
rs7225932	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs7225932	LGALS9C	cis	Whole Blood	GTEx
rs7225932	SHMT1	cis	parietal	SCAN
rs7225932	SHMT1	cis	lymphoblastoid	seeQTL
rs7225932	SHMT1	cis	Artery Aorta	GTEx
rs7225932	LOC162632	cis	parietal	SCAN
rs7225932	FLJ36492	cis	multi-tissue	Pritchard
rs7225932	USP32P2	cis	Whole Blood	GTEx
rs7225932	SHMT1	cis	Esophagus Muscularis	GTEx
rs7225932	SHMT1	cis	Nerve Tibial	GTEx
rs7225932	TOP3A	cis	cerebellum	SCAN

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	chr17:18173000-18213800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:18184800-18217000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr17:18194600-18215600	Weak transcription	Fetal Heart	heart
5	chr17:18195800-18209600	Weak transcription	Psoas Muscle	Psoas
6	chr17:18196800-18217000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:18200600-18211400	Strong transcription	Lung	lung
8	chr17:18201800-18216200	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr17:18202000-18210600	Strong transcription	H9 Cell Line	embryonic stem cell
10	chr17:18202000-18212600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr17:18202000-18213000	Strong transcription	Placenta	Placenta
12	chr17:18202200-18216600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr17:18202400-18208800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:18202400-18210600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr17:18202400-18210800	Strong transcription	Brain Germinal Matrix	brain
16	chr17:18202400-18211200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr17:18202400-18211200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr17:18202400-18211200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr17:18202400-18211200	Strong transcription	Ovary	ovary
20	chr17:18202400-18211200	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr17:18202400-18211200	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr17:18202400-18211200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr17:18202400-18211400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr17:18202400-18211400	Strong transcription	Fetal Muscle Leg	muscle
25	chr17:18202400-18211400	Strong transcription	Left Ventricle	heart
26	chr17:18202400-18211600	Strong transcription	Fetal Intestine Small	intestine
27	chr17:18202400-18211600	Strong transcription	Thymus	Thymus
28	chr17:18202400-18211600	Strong transcription	Osteobl	bone
29	chr17:18202400-18211800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr17:18202400-18211800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr17:18202400-18212000	Strong transcription	Fetal Intestine Large	intestine
32	chr17:18202400-18212200	Strong transcription	Liver	Liver
33	chr17:18202400-18212200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr17:18202400-18212400	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr17:18202400-18212400	Strong transcription	A549	lung
36	chr17:18202400-18212600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr17:18202400-18212600	Strong transcription	Duodenum Mucosa	Duodenum
38	chr17:18202400-18212800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr17:18202400-18213600	Strong transcription	Dnd41	blood
40	chr17:18202400-18214200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr17:18202400-18215400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr17:18202400-18215600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr17:18202400-18215600	Strong transcription	Fetal Thymus	thymus
44	chr17:18202400-18216000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr17:18202400-18216000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr17:18202400-18216000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr17:18202400-18216200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr17:18202400-18216400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr17:18202400-18216400	Strong transcription	Fetal Stomach	stomach
50	chr17:18202400-18216600	Strong transcription	HUES48 Cell Line	embryonic stem cell

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