Variant report

Variant	rs854771
Chromosome Location	chr17:18060192-18060193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr17:18060159-18060361	HepG2	liver:	n/a	chr17:18060172-18060180
2	TBL1XR1	chr17:18059895-18060294	GM12878	blood:	n/a	n/a
3	STAT3	chr17:18060186-18060386	MCF10A-Er-Src	breast:	n/a	n/a
4	MAZ	chr17:18060092-18060275	Hela-S3	cervix:	n/a	chr17:18060171-18060180
5	ZNF143	chr17:18060170-18060330	K562	blood:	n/a	n/a
6	JUND	chr17:18060154-18060318	K562	blood:	n/a	chr17:18060172-18060180
7	MAFK	chr17:18060116-18060301	K562	blood:	n/a	chr17:18060170-18060179 chr17:18060170-18060180

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:18059406..18063498-chr17:18086302..18089651,4	K562	blood:
2	chr17:18041836..18044896-chr17:18058231..18061380,3	K562	blood:
3	chr17:18044305..18045021-chr17:18059355..18060391,3	MCF-7	breast:
4	chr17:18057503..18062681-chr17:18084968..18089396,8	MCF-7	breast:
5	chr17:18054836..18057146-chr17:18057563..18061410,3	MCF-7	breast:
6	chr17:18044150..18045078-chr17:18059256..18060265,3	MCF-7	breast:
7	chr17:18059834..18062065-chr17:18216789..18219409,3	MCF-7	breast:
8	chr17:18057350..18061680-chr17:18083813..18088656,8	K562	blood:
9	chr17:18057330..18058891-chr17:18059852..18061611,2	MCF-7	breast:
10	chr17:18055989..18058847-chr17:18059352..18061809,2	K562	blood:
11	chr17:18059602..18061497-chr17:18162404..18165342,2	MCF-7	breast:
12	chr17:18034463..18036913-chr17:18059459..18061391,2	MCF-7	breast:
13	chr17:18058869..18061487-chr17:18085234..18087160,2	MCF-7	breast:

No data

Variant related genes	Relation type
MYO15A	TF binding region
ENSG00000266677	Chromatin interaction
ENSG00000091542	Chromatin interaction
ENSG00000176994	Chromatin interaction
ENSG00000091536	Chromatin interaction
ENSG00000177427	Chromatin interaction
ENSG00000177302	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11869205	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11870766	0.85[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11871970	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12150618	0.81[CEU][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12451754	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12936694	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]
rs12937300	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs12939469	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12939757	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs12945597	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs12946842	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12952556	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs1378601	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs1378602	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs1563631	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs1979276	0.82[CHD][hapmap]
rs2273028	0.82[CHD][hapmap]
rs2360234	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2605132	0.85[EUR][1000 genomes]
rs2605136	0.96[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs2605137	0.81[AMR][1000 genomes]
rs2605142	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs2746025	0.82[CHD][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs2746027	0.82[CHD][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes]
rs2746030	0.80[AMR][1000 genomes]
rs2925137	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2925138	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4603612	0.81[CEU][hapmap];0.85[CHB][hapmap];0.83[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];0.91[EUR][1000 genomes]
rs4924839	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs4924840	0.81[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4924841	0.81[CEU][hapmap];0.85[CHB][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]
rs4925149	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4925150	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4925171	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs56021431	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs712270	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs712272	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712275	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7207306	0.82[CHD][hapmap]
rs7212808	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7215839	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs8071834	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs8080966	0.83[GIH][hapmap]
rs854772	0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs854775	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs854776	0.86[ASN][1000 genomes]
rs854779	0.91[CHD][hapmap];1.00[JPT][hapmap]
rs854781	1.00[JPT][hapmap]
rs854795	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs854797	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs854798	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs854799	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs854801	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs854804	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs854805	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs854806	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs854807	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs860567	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs860568	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs861278	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs865923	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs921986	0.82[CHD][hapmap]

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	nsv907769	chr17:18000321-18064195	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv470580	chr17:18029857-18060192	Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
11	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
12	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs854771	ALKBH5	cis	Esophagus Muscularis	GTEx
rs854771	MYO15A	cis	cerebellum	SCAN
rs854771	SHMT1	cis	Esophagus Muscularis	GTEx
rs854771	ALKBH5	cis	Artery Tibial	GTEx
rs854771	LLGL1	cis	Esophagus Mucosa	GTEx
rs854771	RP11-258F1.1	cis	Esophagus Muscularis	GTEx
rs854771	LOC162632	cis	parietal	SCAN
rs854771	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs854771	ATPAF2	cis	cerebellum	SCAN
rs854771	LOC162632	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18057200-18061400	Weak transcription	Primary T cells from cord blood	blood
2	chr17:18057400-18060200	Weak transcription	HMEC	breast
3	chr17:18057400-18061000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr17:18057400-18061200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr17:18057400-18061200	Weak transcription	Small Intestine	intestine
6	chr17:18057400-18061400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr17:18057400-18061400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr17:18057600-18060800	Weak transcription	Primary B cells from cord blood	blood
9	chr17:18057600-18060800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr17:18057600-18060800	Weak transcription	Placenta	Placenta
11	chr17:18057600-18061000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr17:18057600-18061000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr17:18057600-18061000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr17:18057600-18061000	Weak transcription	Lung	lung
15	chr17:18057600-18061000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr17:18057600-18061200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr17:18057600-18061200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr17:18057600-18061200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr17:18057600-18061200	Weak transcription	Esophagus	oesophagus
20	chr17:18057600-18061200	Weak transcription	Fetal Intestine Large	intestine
21	chr17:18057600-18061200	Weak transcription	Right Ventricle	heart
22	chr17:18057600-18061400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr17:18057600-18061400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr17:18057600-18061400	Weak transcription	Adipose Nuclei	Adipose
25	chr17:18057600-18061400	Weak transcription	Brain Angular Gyrus	brain
26	chr17:18057600-18061400	Weak transcription	Colonic Mucosa	Colon
27	chr17:18057600-18061400	Weak transcription	Fetal Intestine Small	intestine
28	chr17:18057600-18061400	Weak transcription	Left Ventricle	heart
29	chr17:18057600-18061400	Weak transcription	Pancreas	Pancrea
30	chr17:18057600-18061400	Weak transcription	Right Atrium	heart
31	chr17:18057600-18061400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr17:18057600-18061400	Weak transcription	HUVEC	blood vessel
33	chr17:18057600-18061400	Weak transcription	Osteobl	bone
34	chr17:18057600-18061600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr17:18057600-18061600	Weak transcription	Liver	Liver
36	chr17:18057600-18061600	Weak transcription	Brain Anterior Caudate	brain
37	chr17:18057600-18061600	Weak transcription	Psoas Muscle	Psoas
38	chr17:18057600-18061600	Weak transcription	NH-A	brain
39	chr17:18057600-18061800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr17:18057600-18061800	Weak transcription	NHDF-Ad	bronchial
41	chr17:18057600-18063000	Weak transcription	HSMMtube	muscle
42	chr17:18057800-18060200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr17:18057800-18060600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr17:18057800-18060600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr17:18057800-18060600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr17:18057800-18060600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr17:18057800-18060800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr17:18057800-18061200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr17:18057800-18061200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr17:18057800-18061200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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