Variant report

Variant	rs2955387
Chromosome Location	chr17:18008289-18008290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:18006613-18008711	K562	blood:	n/a	n/a
2	POLR2A	chr17:18008127-18008563	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr17:18008277-18008403	ProgFib	skin:	n/a	n/a
4	POLR2A	chr17:18005959-18008751	K562	blood:	n/a	n/a
5	POLR2A	chr17:18007521-18008481	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr17:18007318-18008318	GM12891	blood:	n/a	n/a
7	POLR2A	chr17:18006013-18009825	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr17:18005830-18008721	GM12892	blood:	n/a	n/a
9	POLR2A	chr17:18007712-18008615	GM12878	blood:	n/a	n/a
10	POLR2A	chr17:18007333-18008767	HepG2	liver:	n/a	n/a
11	POLR2A	chr17:18008224-18008375	A549	lung:	n/a	n/a
12	POLR2A	chr17:18006637-18008767	GM12878	blood:	n/a	n/a
13	POLR2A	chr17:18008123-18008453	GM12891	blood:	n/a	n/a
14	POLR2A	chr17:18008173-18008609	K562	blood:	n/a	n/a
15	POLR2A	chr17:18008239-18008492	K562	blood:	n/a	n/a
16	POLR2A	chr17:18008270-18008664	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr17:18006650-18008578	GM12892	blood:	n/a	n/a
18	POLR2A	chr17:18007924-18008601	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:18007007..18008585-chr17:18011589..18013521,2	MCF-7	breast:
2	chr17:18004673..18008844-chr17:18009305..18012045,5	K562	blood:
3	chr17:18006973..18009716-chr17:18011197..18014211,3	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATPAF2-2	chr17:18007636-18008671	NONHSAT146146
2	lnc-ATPAF2-2	chr17:18007559-18008671	NONHSAT146144
3	lnc-ATPAF2-2	chr17:18007636-18009088	NONHSAT146147

No data

Variant related genes	Relation type
DRG2	TF binding region
MYO15A	TF binding region
ENSG00000091536	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs2272570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925139	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][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]
rs2925140	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925141	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2925142	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2925143	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2955361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955363	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955364	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2955374	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2955375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955386	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2975000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2975001	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2975002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2975003	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2975004	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap];0.92[EUR][1000 genomes]
rs2975005	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.91[EUR][1000 genomes]
rs4513153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925139	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502635	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7225972	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8077176	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv960429	chr17:17951047-18027679	Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	nsv457697	chr17:18003845-18046290	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv574527	chr17:18003845-18046290	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2955387	ATPAF2	cis	Thyroid	GTEx
rs2955387	DRG2	cis	Artery Aorta	GTEx
rs2955387	ATPAF2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17991800-18009800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:17992200-18014000	Weak transcription	Right Atrium	heart
3	chr17:17993000-18012000	Strong transcription	Fetal Muscle Trunk	muscle
4	chr17:17993200-18011200	Strong transcription	Fetal Stomach	stomach
5	chr17:17994000-18010800	Strong transcription	Dnd41	blood
6	chr17:17994200-18010800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr17:17994200-18010800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr17:17994200-18011000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:17994200-18011000	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr17:17994200-18011600	Strong transcription	Fetal Muscle Leg	muscle
11	chr17:17994200-18011800	Strong transcription	Stomach Smooth Muscle	stomach
12	chr17:17994200-18012000	Strong transcription	Fetal Intestine Small	intestine
13	chr17:17994400-18011000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr17:17994400-18011400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr17:17994600-18011200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr17:17994600-18012800	Strong transcription	Thymus	Thymus
17	chr17:17995000-18010800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr17:17995000-18011200	Strong transcription	Placenta	Placenta
19	chr17:17995200-18011000	Strong transcription	Ovary	ovary
20	chr17:17995200-18011000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr17:17995200-18011000	Strong transcription	NHLF	lung
22	chr17:17995200-18011400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr17:17995200-18011400	Strong transcription	Lung	lung
24	chr17:17995200-18011400	Strong transcription	A549	lung
25	chr17:17995200-18011600	Strong transcription	Fetal Intestine Large	intestine
26	chr17:17995400-18011000	Strong transcription	Adipose Nuclei	Adipose
27	chr17:17995400-18011400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr17:17996000-18010400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr17:17996200-18011000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr17:17996400-18011000	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr17:17996800-18011000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr17:17996800-18011200	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr17:17997000-18010800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr17:17997000-18010800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr17:17997000-18010800	Strong transcription	Aorta	Aorta
36	chr17:17997000-18010800	Strong transcription	Brain Anterior Caudate	brain
37	chr17:17997000-18011000	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr17:17997000-18011200	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr17:17997200-18011000	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr17:17997600-18011000	Weak transcription	Fetal Heart	heart
41	chr17:17997600-18011000	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr17:17997800-18008600	Strong transcription	NHEK	skin
43	chr17:17998000-18011000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr17:17998000-18011200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr17:17998000-18011600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr17:17998600-18011200	Strong transcription	Right Ventricle	heart
47	chr17:17998600-18011200	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr17:17999000-18010400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr17:17999000-18011000	Strong transcription	Brain Germinal Matrix	brain
50	chr17:17999000-18011000	Strong transcription	Esophagus	oesophagus

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