Variant report

Variant	rs9913262
Chromosome Location	chr17:18111344-18111345
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18111005..18113844-chr17:18114465..18116043,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12051649	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075657	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2075658	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2245430	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2473656	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2605133	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2856289	0.84[EUR][1000 genomes]
rs4925144	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59588957	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs712271	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs712274	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72831919	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs854773	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs854774	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs854777	0.88[CEU][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs854778	0.81[EUR][1000 genomes]
rs854780	0.81[EUR][1000 genomes]
rs854783	0.81[EUR][1000 genomes]
rs854796	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs854800	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs854802	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs854803	0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9899249	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9903403	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9903591	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1062828	chr17:18098110-18136330	Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv543245	chr17:18098110-18136330	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv907775	chr17:18108496-18206234	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9913262	SHMT1	cis	Whole Blood	GTEx
rs9913262	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs9913262	SHMT1	cis	Esophagus Muscularis	GTEx
rs9913262	SHMT1	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18091400-18114000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:18091800-18114400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr17:18094200-18114600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr17:18094400-18114600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr17:18094600-18114600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:18095000-18114600	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:18095000-18114800	Strong transcription	Fetal Thymus	thymus
8	chr17:18095400-18116000	Strong transcription	Fetal Stomach	stomach
9	chr17:18095600-18114600	Strong transcription	Dnd41	blood
10	chr17:18096200-18114400	Strong transcription	Primary T cells from cord blood	blood
11	chr17:18096200-18114600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr17:18096800-18114600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr17:18097000-18114600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr17:18097200-18114600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr17:18097600-18114600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr17:18097800-18114600	Strong transcription	Fetal Brain Female	brain
17	chr17:18098000-18114600	Strong transcription	Primary B cells from cord blood	blood
18	chr17:18098000-18114600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr17:18098000-18114600	Strong transcription	Fetal Muscle Leg	muscle
20	chr17:18101200-18114400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr17:18101600-18114600	Strong transcription	Thymus	Thymus
22	chr17:18101600-18115400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr17:18102000-18114600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr17:18102000-18116200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr17:18102200-18114600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr17:18102400-18114400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr17:18103000-18114600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:18103000-18114800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr17:18103400-18114400	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr17:18104000-18114600	Strong transcription	Spleen	Spleen
31	chr17:18104200-18114400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr17:18104600-18114600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr17:18104800-18116400	Weak transcription	Psoas Muscle	Psoas
34	chr17:18105600-18114400	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr17:18105600-18114600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr17:18105600-18114600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr17:18105800-18114600	Strong transcription	Adipose Nuclei	Adipose
38	chr17:18105800-18114600	Strong transcription	GM12878-XiMat	blood
39	chr17:18105800-18114800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr17:18105800-18114800	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr17:18106400-18114600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr17:18106600-18114200	Strong transcription	NH-A	brain
43	chr17:18106600-18114600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr17:18106600-18114600	Strong transcription	NHEK	skin
45	chr17:18106800-18113800	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr17:18106800-18114600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr17:18106800-18114600	Strong transcription	Ovary	ovary
48	chr17:18107000-18112200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr17:18107000-18112200	Weak transcription	Stomach Mucosa	stomach
50	chr17:18107200-18111800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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