Variant report

Variant	rs854803
Chromosome Location	chr17:18089230-18089231
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	BATF	chr17:18089091-18089467	GM12878	blood:	n/a	chr17:18089334-18089344
2	CHD1	chr17:18085856-18091134	IMR90	lung:	n/a	n/a
3	MXI1	chr17:18085581-18092228	SK-N-SH	brain:	n/a	chr17:18086672-18086687 chr17:18088362-18088377
4	BHLHE40	chr17:18089219-18089823	K562	blood:	n/a	n/a
5	MXI1	chr17:18088864-18090037	GM12878	blood:	n/a	n/a
6	POLR2A	chr17:18089079-18089552	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr17:18088811-18089707	U87	brain:	n/a	n/a
8	EP300	chr17:18087589-18092262	SK-N-SH	brain:	n/a	chr17:18089998-18090012
9	WRNIP1	chr17:18087774-18091201	GM12878	blood:	n/a	n/a
10	MYC	chr17:18088495-18090406	MCF10A-Er-Src	breast:	n/a	chr17:18089982-18089991
11	UBTF	chr17:18089183-18089383	K562	blood:	n/a	n/a
12	BATF	chr17:18089226-18089450	GM12878	blood:	n/a	chr17:18089334-18089344
13	POLR2A	chr17:18088913-18090416	K562	blood:	n/a	n/a
14	UBTF	chr17:18088896-18089575	K562	blood:	n/a	n/a
15	FOXM1	chr17:18088996-18089477	GM12878	blood:	n/a	n/a
16	RUNX3	chr17:18089012-18089560	GM12878	blood:	n/a	n/a
17	KAP1	chr17:18087725-18091513	HEK293	kidney:	n/a	chr17:18091056-18091064
18	POLR2A	chr17:18088902-18089543	GM12878	blood:	n/a	n/a
19	POLR2A	chr17:18089120-18089590	GM12878	blood:	n/a	n/a
20	YY1	chr17:18089211-18089583	GM12878	blood:	n/a	chr17:18089439-18089461
21	EBF1	chr17:18089125-18089528	GM12878	blood:	n/a	chr17:18089374-18089385
22	POLR2A	chr17:18089030-18089263	MCF10A-Er-Src	breast:	n/a	n/a
23	EBF1	chr17:18088782-18089554	GM12878	blood:	n/a	chr17:18088851-18088860 chr17:18089374-18089385
24	MTA3	chr17:18089037-18089746	GM12878	blood:	n/a	n/a
25	EBF1	chr17:18089176-18089552	GM12878	blood:	n/a	chr17:18089374-18089385
26	POLR2A	chr17:18085568-18089598	IMR90	lung:	n/a	n/a
27	FOS	chr17:18089212-18090225	MCF10A-Er-Src	breast:	n/a	chr17:18089337-18089345 chr17:18089336-18089346 chr17:18089336-18089346
28	MXI1	chr17:18086003-18091020	IMR90	lung:	n/a	chr17:18086672-18086687 chr17:18088362-18088377
29	ATF2	chr17:18089089-18089603	GM12878	blood:	n/a	n/a
30	NFIC	chr17:18088903-18089613	GM12878	blood:	n/a	n/a
31	CHD1	chr17:18086161-18089744	GM12878	blood:	n/a	n/a
32	JUND	chr17:18089159-18090082	K562	blood:	n/a	chr17:18089337-18089345 chr17:18089336-18089346 chr17:18089336-18089346
33	POLR2A	chr17:18089148-18089688	U87	brain:	n/a	n/a
34	RUNX3	chr17:18088896-18089732	GM12878	blood:	n/a	n/a
35	MAFK	chr17:18088842-18089297	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:18088851..18092330-chr17:18106978..18109728,3	K562	blood:
2	chr17:18057503..18062681-chr17:18084968..18089396,8	MCF-7	breast:
3	chr17:18085197..18089449-chr17:18160313..18164902,6	K562	blood:
4	chr17:18059406..18063498-chr17:18086302..18089651,4	K562	blood:
5	chr17:18061742..18067292-chr17:18083221..18089651,7	K562	blood:
6	chr17:18088345..18089995-chr17:18161627..18163535,2	K562	blood:
7	chr17:18088174..18090098-chr17:18107695..18110027,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266677	TF binding region
ENSG00000177427	Chromatin interaction
ENSG00000091542	Chromatin interaction
ENSG00000091536	Chromatin interaction
ENSG00000177731	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs12051649	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12946752	0.84[GIH][hapmap]
rs1563632	0.84[GIH][hapmap]
rs1563634	0.84[GIH][hapmap]
rs2075657	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075658	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2245430	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2280777	0.84[CHD][hapmap]
rs2473656	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs2605133	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2605141	0.84[GIH][hapmap]
rs2605144	0.85[GIH][hapmap]
rs2856289	0.81[EUR][1000 genomes]
rs4925144	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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];1.00[ASN][1000 genomes]
rs59588957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712271	1.00[CEU][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs712274	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7225932	0.84[GIH][hapmap]
rs72831919	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs854773	1.00[CEU][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs854774	1.00[CEU][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs854777	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs854778	0.86[EUR][1000 genomes]
rs854780	0.85[EUR][1000 genomes]
rs854783	0.85[EUR][1000 genomes]
rs854796	0.99[ASN][1000 genomes]
rs854800	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854802	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9899249	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9903403	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9903591	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9913262	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]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv907771	chr17:18013560-18098018	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv907772	chr17:18030524-18098018	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	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
11	esv3411665	chr17:18085527-18089325	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs854803	LOC162632	cis	parietal	SCAN
rs854803	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs854803	MYO15A	cis	parietal	SCAN
rs854803	LOC162632	cis	cerebellum	SCAN
rs854803	SHMT1	cis	Lymphoblastoid	GTEx
rs854803	SHMT1	cis	parietal	SCAN
rs854803	TOP3A	cis	cerebellum	SCAN
rs854803	SHMT1	cis	Nerve Tibial	GTEx
rs854803	SHMT1	cis	Whole Blood	GTEx
rs854803	SHMT1	cis	lymphoblastoid	seeQTL
rs854803	SHMT1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18085600-18090600	Active TSS	Aorta	Aorta
2	chr17:18085800-18089400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr17:18085800-18090200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr17:18085800-18090600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr17:18086000-18089400	Active TSS	GM12878-XiMat	blood
6	chr17:18086000-18090000	Active TSS	Pancreas	Pancrea
7	chr17:18086000-18090200	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr17:18086000-18090200	Active TSS	Ovary	ovary
9	chr17:18086200-18089400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr17:18087400-18089400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:18087400-18089400	Active TSS	Right Atrium	heart
12	chr17:18087600-18090200	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr17:18087800-18089400	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr17:18087800-18089400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
15	chr17:18087800-18089400	Bivalent/Poised TSS	HepG2	liver
16	chr17:18087800-18090400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr17:18087800-18091200	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr17:18087800-18092000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr17:18087800-18092200	Transcr. at gene 5' and 3'	Dnd41	blood
20	chr17:18088000-18089800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
21	chr17:18088000-18090000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr17:18088000-18090400	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr17:18088000-18090800	Flanking Active TSS	Liver	Liver
24	chr17:18088000-18091200	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
25	chr17:18088000-18091800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr17:18088000-18092000	Flanking Active TSS	HUVEC	blood vessel
27	chr17:18088000-18093000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr17:18088200-18090400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
29	chr17:18088200-18090400	Flanking Active TSS	Placenta	Placenta
30	chr17:18088200-18090600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:18088200-18090600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr17:18088200-18090600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr17:18088200-18090600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr17:18088200-18090800	Flanking Active TSS	Fetal Brain Female	brain
35	chr17:18088200-18091000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr17:18088200-18091000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
37	chr17:18088200-18091200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr17:18088200-18091200	Flanking Active TSS	Fetal Brain Male	brain
39	chr17:18088200-18091400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr17:18088200-18091400	Transcr. at gene 5' and 3'	Thymus	Thymus
41	chr17:18088200-18092000	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr17:18088200-18092000	Flanking Active TSS	NH-A	brain
43	chr17:18088400-18090200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr17:18088400-18090200	Enhancers	Spleen	Spleen
45	chr17:18088400-18091200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr17:18088600-18089400	Active TSS	Colonic Mucosa	Colon
47	chr17:18088600-18089400	Active TSS	Fetal Muscle Trunk	muscle
48	chr17:18088600-18089600	Active TSS	HSMMtube	muscle
49	chr17:18088600-18090000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr17:18088600-18091000	Flanking Active TSS	Brain Substantia Nigra	brain

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