Variant report

Variant	rs2955361
Chromosome Location	chr17:18013560-18013561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:18008903..18011616-chr17:18013439..18016712,4	K562	blood:
2	chr17:18012129..18016581-chr17:18018314..18021860,5	K562	blood:
3	chr17:18013158..18015444-chr17:18018445..18021397,3	MCF-7	breast:
4	chr17:18012199..18014254-chr17:18015114..18017302,2	K562	blood:
5	chr17:18008903..18011333-chr17:18013439..18016712,3	K562	blood:
6	chr17:18006973..18009716-chr17:18011197..18014211,3	MCF-7	breast:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATPAF2-2	chr17:18012668-18014598	NONHSAT146146
2	lnc-ATPAF2-2	chr17:18012924-18014521	NONHSAT146144
3	lnc-ATPAF2-2	chr17:18012668-18013771	NONHSAT146145
4	lnc-ATPAF2-2	chr17:18010648-18013777	NONHSAT146149
5	lnc-ATPAF2-2	chr17:18009717-18014392	NONHSAT146147

No data

Variant related genes	Relation type
ENSG00000108591	Chromatin interaction

Extended variants
information (count: 36 )
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];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925139	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]
rs2925140	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925141	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2925142	0.86[CHD][hapmap];0.88[GIH][hapmap];0.82[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]
rs2955362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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];0.93[JPT][hapmap];0.95[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	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][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];0.87[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955387	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]
rs2975000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[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[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[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];0.87[JPT][hapmap];0.86[TSI][hapmap];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];0.93[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];0.87[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502635	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7225972	0.91[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: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	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
12	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2955361	ATPAF2	cis	Heart Left Ventricle	GTEx
rs2955361	DRG2	cis	Artery Aorta	GTEx
rs2955361	ATPAF2	cis	Thyroid	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17992200-18014000	Weak transcription	Right Atrium	heart
2	chr17:18002400-18019600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr17:18003200-18021000	Weak transcription	Psoas Muscle	Psoas
4	chr17:18003800-18015200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr17:18004800-18015400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr17:18005400-18013600	Weak transcription	HSMM	muscle
7	chr17:18005400-18017000	Weak transcription	HepG2	liver
8	chr17:18005600-18015000	Weak transcription	HMEC	breast
9	chr17:18005800-18014800	Weak transcription	HSMMtube	muscle
10	chr17:18009000-18015000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:18010200-18014200	Genic enhancers	Liver	Liver
12	chr17:18010200-18015000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr17:18010600-18015400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr17:18010600-18015800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr17:18010600-18030400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:18010800-18014000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr17:18010800-18015400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr17:18010800-18020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr17:18011000-18013800	Weak transcription	NHLF	lung
20	chr17:18011000-18014800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr17:18011000-18015000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr17:18011000-18015000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr17:18011000-18015200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:18011000-18017200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:18011000-18018000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr17:18011000-18022600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr17:18011200-18013600	Weak transcription	Brain Hippocampus Middle	brain
28	chr17:18011200-18014800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr17:18011200-18015000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr17:18011200-18018000	Weak transcription	Right Ventricle	heart
31	chr17:18011200-18019400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr17:18011200-18022000	Weak transcription	Placenta	Placenta
33	chr17:18011200-18026200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr17:18011400-18014000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:18011400-18014000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr17:18011400-18015200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:18011600-18013600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr17:18011600-18014800	Weak transcription	Fetal Muscle Leg	muscle
39	chr17:18011600-18015000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:18011800-18014200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr17:18011800-18018200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr17:18012000-18014000	Weak transcription	Fetal Intestine Small	intestine
43	chr17:18012000-18014800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr17:18012200-18016400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr17:18012400-18014000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr17:18012400-18015200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr17:18012800-18013600	Weak transcription	Thymus	Thymus
48	chr17:18012800-18014000	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr17:18012800-18014800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr17:18013000-18013800	Weak transcription	Spleen	Spleen

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