Variant report

Variant	rs2955386
Chromosome Location	chr17:17999673-17999674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17999260..18001895-chr17:18003244..18006001,2	K562	blood:
2	chr17:17999192..18001070-chr17:18003936..18005564,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2272570	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][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]
rs2925139	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]
rs2925140	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925141	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2925142	0.81[JPT][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];0.86[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955362	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955363	1.00[CEU][hapmap];1.00[JPT][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]
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];0.86[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955387	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];0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2975001	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2975002	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][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];0.92[EUR][1000 genomes]
rs2975005	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4513153	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs6502635	0.92[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:7 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2955386	ATPAF2	cis	Thyroid	GTEx
rs2955386	DRG2	cis	Artery Aorta	GTEx
rs2955386	ATPAF2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:125 , 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	chr17:17992000-18000600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:17992200-18000800	Weak transcription	Psoas Muscle	Psoas
4	chr17:17992200-18002400	Weak transcription	Fetal Brain Male	brain
5	chr17:17992200-18014000	Weak transcription	Right Atrium	heart
6	chr17:17992400-17999800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:17992400-18001000	Weak transcription	Colon Smooth Muscle	Colon
8	chr17:17992400-18005600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:17993000-18004800	Weak transcription	Small Intestine	intestine
10	chr17:17993000-18012000	Strong transcription	Fetal Muscle Trunk	muscle
11	chr17:17993200-18011200	Strong transcription	Fetal Stomach	stomach
12	chr17:17993800-18005200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr17:17994000-18005400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr17:17994000-18005600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:17994000-18006000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr17:17994000-18010800	Strong transcription	Dnd41	blood
17	chr17:17994200-18005400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr17:17994200-18005600	Strong transcription	Primary T cells from cord blood	blood
19	chr17:17994200-18010800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr17:17994200-18010800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr17:17994200-18011000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:17994200-18011000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr17:17994200-18011600	Strong transcription	Fetal Muscle Leg	muscle
24	chr17:17994200-18011800	Strong transcription	Stomach Smooth Muscle	stomach
25	chr17:17994200-18012000	Strong transcription	Fetal Intestine Small	intestine
26	chr17:17994400-18005600	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr17:17994400-18005600	Strong transcription	Fetal Thymus	thymus
28	chr17:17994400-18011000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr17:17994400-18011400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr17:17994600-18011200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr17:17994600-18012800	Strong transcription	Thymus	Thymus
32	chr17:17994800-18004600	Strong transcription	Liver	Liver
33	chr17:17994800-18005400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr17:17995000-18005600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr17:17995000-18010800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr17:17995000-18011200	Strong transcription	Placenta	Placenta
37	chr17:17995200-18005600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr17:17995200-18011000	Strong transcription	Ovary	ovary
39	chr17:17995200-18011000	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr17:17995200-18011000	Strong transcription	NHLF	lung
41	chr17:17995200-18011400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr17:17995200-18011400	Strong transcription	Lung	lung
43	chr17:17995200-18011400	Strong transcription	A549	lung
44	chr17:17995200-18011600	Strong transcription	Fetal Intestine Large	intestine
45	chr17:17995400-18004800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr17:17995400-18005600	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr17:17995400-18005600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr17:17995400-18011000	Strong transcription	Adipose Nuclei	Adipose
49	chr17:17995400-18011400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr17:17995600-18001400	Strong transcription	Spleen	Spleen

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