Variant report

Variant	rs12936694
Chromosome Location	chr17:18099962-18099963
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18093548..18096318-chr17:18098737..18101675,3	MCF-7	breast:
2	chr17:18092817..18094681-chr17:18097736..18100155,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11869205	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870766	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11871970	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12150618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451754	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12937300	0.90[CHD][hapmap];0.92[GIH][hapmap];0.81[MKK][hapmap]
rs12939469	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12939757	0.90[CHD][hapmap];0.92[GIH][hapmap]
rs12945597	0.90[CHD][hapmap];0.92[GIH][hapmap]
rs12946842	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12952556	0.90[CHD][hapmap];0.92[GIH][hapmap]
rs1378601	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1378602	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1563631	0.90[CHD][hapmap];0.92[GIH][hapmap]
rs1979276	0.90[CHD][hapmap];0.84[GIH][hapmap]
rs2273028	0.90[CHD][hapmap];0.84[GIH][hapmap]
rs2360234	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2461838	0.90[CHD][hapmap]
rs2605132	0.90[EUR][1000 genomes]
rs2605136	0.81[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2605137	0.88[CEU][hapmap];0.88[AMR][1000 genomes]
rs2605142	0.90[CHD][hapmap];0.92[GIH][hapmap]
rs2746025	0.90[CHD][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap]
rs2746027	0.82[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes]
rs2746030	0.87[AMR][1000 genomes]
rs28641923	0.96[ASN][1000 genomes]
rs2925137	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925138	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794782	0.86[JPT][hapmap]
rs4603612	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924839	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4924840	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924841	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925150	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925171	0.90[CHD][hapmap];0.92[GIH][hapmap]
rs56021431	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643333	0.90[CHD][hapmap]
rs712270	0.92[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs712272	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs712273	0.90[ASN][1000 genomes]
rs712275	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7207123	0.81[CHD][hapmap];0.84[GIH][hapmap]
rs7207306	0.90[CHD][hapmap]
rs7212808	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7215839	0.90[CHD][hapmap];0.92[GIH][hapmap]
rs8071834	1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8080966	0.88[GIH][hapmap]
rs854771	0.81[CEU][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs854772	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs854775	0.86[JPT][hapmap]
rs854779	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs854781	0.86[JPT][hapmap]
rs854795	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs854797	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs854798	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854799	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs854801	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854804	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs854805	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854806	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854807	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs860567	0.92[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs860568	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs861278	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs865923	0.86[JPT][hapmap]
rs921986	0.90[CHD][hapmap];0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12936694	ALKBH5	cis	Esophagus Muscularis	GTEx
rs12936694	MYO15A	cis	cerebellum	SCAN
rs12936694	LLGL1	cis	Esophagus Mucosa	GTEx
rs12936694	LOC162632	cis	parietal	SCAN
rs12936694	SHMT1	cis	Artery Tibial	GTEx
rs12936694	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs12936694	SHMT1	cis	Muscle Skeletal	GTEx
rs12936694	ATPAF2	cis	cerebellum	SCAN
rs12936694	SHMT1	cis	Esophagus Muscularis	GTEx
rs12936694	LGALS9C	cis	Whole Blood	GTEx
rs12936694	LOC162632	cis	cerebellum	SCAN
rs12936694	RP11-258F1.1	cis	Esophagus Muscularis	GTEx
rs12936694	SHMT1	cis	parietal	SCAN
rs12936694	ALKBH5	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18090200-18103400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18090800-18104000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:18091200-18104600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr17:18091400-18114000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:18091800-18114400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr17:18092000-18104000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr17:18094200-18114600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr17:18094400-18114600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr17:18094600-18114600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:18094800-18101800	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr17:18094800-18103400	Strong transcription	Fetal Intestine Large	intestine
12	chr17:18095000-18108600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr17:18095000-18114600	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr17:18095000-18114800	Strong transcription	Fetal Thymus	thymus
15	chr17:18095200-18101000	Strong transcription	Thymus	Thymus
16	chr17:18095400-18101800	Weak transcription	Small Intestine	intestine
17	chr17:18095400-18116000	Strong transcription	Fetal Stomach	stomach
18	chr17:18095600-18100600	Strong transcription	GM12878-XiMat	blood
19	chr17:18095600-18103600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr17:18095600-18114600	Strong transcription	Dnd41	blood
21	chr17:18095800-18100400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr17:18095800-18102200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr17:18095800-18103200	Strong transcription	Fetal Intestine Small	intestine
24	chr17:18095800-18108600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr17:18096200-18101600	Strong transcription	Fetal Muscle Trunk	muscle
26	chr17:18096200-18114400	Strong transcription	Primary T cells from cord blood	blood
27	chr17:18096200-18114600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:18096400-18100400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr17:18096400-18104800	Strong transcription	Hela-S3	cervix
30	chr17:18096800-18104400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr17:18096800-18114600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr17:18097000-18102000	Strong transcription	HepG2	liver
33	chr17:18097000-18102000	Strong transcription	K562	blood
34	chr17:18097000-18102600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr17:18097000-18105000	Strong transcription	A549	lung
36	chr17:18097000-18108600	Strong transcription	Brain Germinal Matrix	brain
37	chr17:18097000-18114600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr17:18097200-18100600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr17:18097200-18100600	Strong transcription	Liver	Liver
40	chr17:18097200-18114600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr17:18097400-18100600	Strong transcription	Adipose Nuclei	Adipose
42	chr17:18097400-18101200	Strong transcription	Brain Hippocampus Middle	brain
43	chr17:18097600-18100600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr17:18097600-18114600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr17:18097800-18100600	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr17:18097800-18100600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr17:18097800-18100600	Strong transcription	Lung	lung
48	chr17:18097800-18101000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr17:18097800-18101200	Strong transcription	NHDF-Ad	bronchial
50	chr17:18097800-18102400	Strong transcription	NHLF	lung

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