Variant report

Variant	rs3794771
Chromosome Location	chr17:18217186-18217187
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT1	chr17:18216992-18218847	Hela-S3	cervix:	n/a	chr17:18217642-18217656
2	POLR2A	chr17:18217023-18217319	K562	blood:	n/a	n/a
3	REST	chr17:18217025-18219150	A549	lung:	n/a	chr17:18217230-18217239
4	WRNIP1	chr17:18217046-18218890	GM12878	blood:	n/a	n/a
5	MYC	chr17:18217089-18219045	K562	blood:	n/a	chr17:18218604-18218613
6	MXI1	chr17:18216816-18219173	SK-N-SH	brain:	n/a	n/a
7	MAX	chr17:18217117-18219212	A549	lung:	n/a	chr17:18218604-18218613
8	TBP	chr17:18216999-18219043	K562	blood:	n/a	n/a
9	MXI1	chr17:18216839-18219602	IMR90	lung:	n/a	n/a
10	CTCF	chr17:18217060-18217210	AG09309	skin:	n/a	n/a
11	BRCA1	chr17:18217138-18217755	GM12878	blood:	n/a	n/a
12	HCFC1	chr17:18217119-18219411	Hela-S3	cervix:	n/a	n/a
13	CUX1	chr17:18216975-18217497	GM12878	blood:	n/a	n/a
14	BRCA1	chr17:18217146-18217718	HepG2	liver:	n/a	n/a
15	SIN3AK20	chr17:18217174-18219107	MCF-7	breast:	n/a	n/a
16	SMC3	chr17:18216746-18218789	Hela-S3	cervix:	n/a	n/a
17	UBTF	chr17:18217101-18217285	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:18204042..18206073-chr17:18215565..18218215,2	MCF-7	breast:
2	chr17:18059834..18062065-chr17:18216789..18219409,3	MCF-7	breast:
3	chr17:18207672..18211933-chr17:18214098..18218432,6	MCF-7	breast:
4	chr17:18185665..18188160-chr17:18215584..18219242,3	MCF-7	breast:
5	chr17:18159194..18166260-chr17:18215929..18222740,16	MCF-7	breast:
6	chr17:18156705..18166530-chr17:18215131..18220177,19	MCF-7	breast:
7	chr17:18127269..18131326-chr17:18216439..18220320,6	MCF-7	breast:

No data

Variant related genes	Relation type
SMCR8	TF binding region
ENSG00000131899	Chromatin interaction
ENSG00000177302	Chromatin interaction
ENSG00000091536	Chromatin interaction
ENSG00000177731	Chromatin interaction
ENSG00000177427	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11868259	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11870126	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12936652	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12936769	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12937300	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12939092	0.82[EUR][1000 genomes]
rs12939259	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939357	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939757	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12945597	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12946058	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12949078	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949983	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12952556	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12952667	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1563631	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1563633	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979276	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979277	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2230154	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273028	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2273030	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386456	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2386457	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2386458	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605142	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746023	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746024	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28419113	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764405	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3783	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3794772	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3829583	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4632181	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924750	0.81[EUR][1000 genomes]
rs4924842	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924843	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4924845	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924847	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924849	0.83[EUR][1000 genomes]
rs4925160	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925162	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925163	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925167	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925169	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925171	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925172	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58215032	0.90[EUR][1000 genomes]
rs6502643	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502644	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502646	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502649	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66903818	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207123	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215839	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7222684	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7223122	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068602	0.87[EUR][1000 genomes]
rs8068854	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070633	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8071231	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073464	0.83[EUR][1000 genomes]
rs8074444	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8080966	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921865	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921866	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921986	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs941451	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9898631	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3794771	SHMT1	cis	Muscle Skeletal	GTEx
rs3794771	LGALS9C	cis	Whole Blood	GTEx
rs3794771	SHMT1	cis	multi-tissue	Pritchard
rs3794771	SHMT1	cis	Artery Tibial	GTEx
rs3794771	SHMT1	cis	Esophagus Muscularis	GTEx
rs3794771	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs3794771	LLGL1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 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	chr17:18210600-18217200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:18211200-18217200	Weak transcription	Aorta	Aorta
4	chr17:18215400-18217200	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr17:18215400-18217200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr17:18215400-18217400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr17:18215400-18217400	Transcr. at gene 5' and 3'	Dnd41	blood
8	chr17:18215600-18217200	Enhancers	Colon Smooth Muscle	Colon
9	chr17:18215600-18217200	Enhancers	Fetal Heart	heart
10	chr17:18216000-18217200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:18216000-18217200	Enhancers	Primary T cells fromperipheralblood	blood
12	chr17:18216000-18217400	Flanking Active TSS	GM12878-XiMat	blood
13	chr17:18216200-18217200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr17:18216200-18217200	Enhancers	Primary T cells from cord blood	blood
15	chr17:18216200-18217200	Enhancers	Liver	Liver
16	chr17:18216200-18217200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr17:18216200-18217400	Enhancers	Spleen	Spleen
18	chr17:18216400-18217200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr17:18216400-18217200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr17:18216400-18217200	Enhancers	Primary hematopoietic stem cells	blood
21	chr17:18216400-18217200	Enhancers	Placenta	Placenta
22	chr17:18216400-18217200	Enhancers	Small Intestine	intestine
23	chr17:18216400-18217200	Transcr. at gene 5' and 3'	A549	lung
24	chr17:18216400-18217200	Flanking Active TSS	HepG2	liver
25	chr17:18216400-18217200	Flanking Active TSS	NHDF-Ad	bronchial
26	chr17:18216400-18217400	Enhancers	Primary B cells from peripheral blood	blood
27	chr17:18216400-18217400	Flanking Active TSS	NHLF	lung
28	chr17:18216400-18217600	Flanking Active TSS	HUVEC	blood vessel
29	chr17:18216400-18217800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr17:18216400-18218200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr17:18216600-18217200	Enhancers	Pancreas	Pancrea
32	chr17:18216600-18217200	Flanking Active TSS	HMEC	breast
33	chr17:18216600-18217400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr17:18216600-18217400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr17:18216600-18217400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr17:18216600-18217400	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr17:18216600-18217400	Enhancers	Placenta Amnion	Placenta Amnion
38	chr17:18216600-18217600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr17:18216600-18217600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr17:18216600-18217600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr17:18216600-18217600	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr17:18216600-18217600	Flanking Active TSS	Fetal Brain Male	brain
43	chr17:18216600-18217600	Flanking Active TSS	Fetal Lung	lung
44	chr17:18216600-18217600	Flanking Active TSS	Thymus	Thymus
45	chr17:18216600-18217600	Flanking Active TSS	NH-A	brain
46	chr17:18216600-18217600	Flanking Active TSS	Osteobl	bone
47	chr17:18216600-18217800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr17:18216600-18217800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr17:18216600-18218000	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr17:18216600-18218000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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