Variant report

Variant	rs2975005
Chromosome Location	chr17:17995907-17995908
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17991646..17993233-chr17:17995608..17997950,2	K562	blood:
2	chr17:17991305..17993918-chr17:17994644..17998089,4	K562	blood:
3	chr17:17980284..17981846-chr17:17994472..17997044,2	K562	blood:
4	chr17:17995313..17997784-chr17:18005282..18007698,2	K562	blood:
5	chr17:17989895..17993133-chr17:17993965..17998692,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108591	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs2056842	0.82[ASN][1000 genomes]
rs2272570	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2925139	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.91[EUR][1000 genomes]
rs2925140	0.91[EUR][1000 genomes]
rs2925141	0.89[EUR][1000 genomes]
rs2925142	0.88[GIH][hapmap];0.89[EUR][1000 genomes]
rs2925143	0.89[EUR][1000 genomes]
rs2955361	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.91[EUR][1000 genomes]
rs2955362	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2955363	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2955364	0.89[EUR][1000 genomes]
rs2955374	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2955375	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.92[EUR][1000 genomes]
rs2955386	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2955387	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.91[EUR][1000 genomes]
rs2974998	0.82[ASN][1000 genomes]
rs2974999	0.82[ASN][1000 genomes]
rs2975000	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.85[EUR][1000 genomes]
rs2975001	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.89[EUR][1000 genomes]
rs2975002	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2975003	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2975004	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4365346	0.81[ASN][1000 genomes]
rs4513153	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4925139	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6502635	0.92[EUR][1000 genomes]
rs6502636	0.81[ASN][1000 genomes]
rs6502637	0.82[ASN][1000 genomes]
rs6826	0.81[ASN][1000 genomes]
rs7212447	0.82[ASN][1000 genomes]
rs721669	0.81[ASN][1000 genomes]
rs8077176	0.92[EUR][1000 genomes]
rs854763	0.81[ASN][1000 genomes]
rs854808	0.81[ASN][1000 genomes]
rs854809	0.81[ASN][1000 genomes]
rs854814	0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2975005	ATPAF2	cis	Thyroid	GTEx
rs2975005	DRG2	cis	Artery Aorta	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17991800-17997000	Weak transcription	Aorta	Aorta
2	chr17:17991800-18009800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:17992000-18000600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:17992200-17997000	Weak transcription	Fetal Heart	heart
5	chr17:17992200-18000800	Weak transcription	Psoas Muscle	Psoas
6	chr17:17992200-18002400	Weak transcription	Fetal Brain Male	brain
7	chr17:17992200-18014000	Weak transcription	Right Atrium	heart
8	chr17:17992400-17996000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr17:17992400-17996200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr17:17992400-17996200	Weak transcription	HSMMtube	muscle
11	chr17:17992400-17996200	Weak transcription	Osteobl	bone
12	chr17:17992400-17996400	Weak transcription	Brain Germinal Matrix	brain
13	chr17:17992400-17996800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr17:17992400-17996800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr17:17992400-17997000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr17:17992400-17997000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr17:17992400-17997000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr17:17992400-17997000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr17:17992400-17997000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr17:17992400-17997000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr17:17992400-17997000	Weak transcription	Brain Angular Gyrus	brain
22	chr17:17992400-17997000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr17:17992400-17997000	Weak transcription	Fetal Lung	lung
24	chr17:17992400-17997000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr17:17992400-17997000	Weak transcription	Right Ventricle	heart
26	chr17:17992400-17997000	Weak transcription	Stomach Mucosa	stomach
27	chr17:17992400-17997000	Weak transcription	NH-A	brain
28	chr17:17992400-17997200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr17:17992400-17997200	Weak transcription	Brain Substantia Nigra	brain
30	chr17:17992400-17997200	Weak transcription	Colonic Mucosa	Colon
31	chr17:17992400-17997200	Weak transcription	Fetal Brain Female	brain
32	chr17:17992400-17997200	Weak transcription	Fetal Kidney	kidney
33	chr17:17992400-17997200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr17:17992400-17997400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr17:17992400-17998400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr17:17992400-17998800	Weak transcription	HUVEC	blood vessel
37	chr17:17992400-17999000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr17:17992400-17999800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr17:17992400-18001000	Weak transcription	Colon Smooth Muscle	Colon
40	chr17:17992400-18005600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr17:17992600-17997000	Weak transcription	Pancreas	Pancrea
42	chr17:17992600-17997000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr17:17992600-17997200	Weak transcription	NHDF-Ad	bronchial
44	chr17:17993000-17997000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr17:17993000-17997200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr17:17993000-18004800	Weak transcription	Small Intestine	intestine
47	chr17:17993000-18012000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr17:17993200-17996400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr17:17993200-17997000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr17:17993200-17997000	Weak transcription	Brain Hippocampus Middle	brain

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