Variant report

Variant	rs11656629
Chromosome Location	chr17:17907768-17907769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr17:17907524-17908962	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr17:17907677-17907889	HepG2	liver:	n/a	n/a
3	POLR2A	chr17:17907594-17908693	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17901247..17903124-chr17:17907149..17909889,2	MCF-7	breast:
2	chr17:17739486..17742070-chr17:17906240..17907771,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATPAF2-1	chr17:17907231-17909643	NONHSAT146130

Variant related genes	Relation type
ENSG00000201378	TF binding region
LRRC48	TF binding region
ENSG00000072310	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11652819	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11652861	1.00[CHB][hapmap];1.00[LWK][hapmap]
rs11653007	1.00[CEU][hapmap]
rs11654240	0.90[EUR][1000 genomes]
rs11656725	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11658804	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12603505	1.00[LWK][hapmap]
rs16960959	1.00[CHB][hapmap]
rs33997182	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34434158	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3677	1.00[LWK][hapmap]
rs60743050	1.00[EUR][1000 genomes]
rs8072048	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	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
5	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17876600-17914600	Weak transcription	Aorta	Aorta
2	chr17:17876800-17909400	Weak transcription	Brain Substantia Nigra	brain
3	chr17:17876800-17912000	Weak transcription	Colon Smooth Muscle	Colon
4	chr17:17881800-17908200	Weak transcription	Pancreas	Pancrea
5	chr17:17886800-17909400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr17:17886800-17913000	Weak transcription	Fetal Lung	lung
7	chr17:17892200-17908400	Weak transcription	Lung	lung
8	chr17:17892400-17910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr17:17892600-17909800	Weak transcription	Brain Angular Gyrus	brain
10	chr17:17892800-17908000	Weak transcription	Spleen	Spleen
11	chr17:17894000-17920600	Weak transcription	Stomach Mucosa	stomach
12	chr17:17894600-17911400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr17:17895200-17909600	Weak transcription	NHLF	lung
14	chr17:17898000-17909200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr17:17898000-17910800	Weak transcription	Brain Hippocampus Middle	brain
16	chr17:17898200-17908200	Weak transcription	Right Ventricle	heart
17	chr17:17898200-17908400	Weak transcription	Fetal Brain Female	brain
18	chr17:17898200-17909000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr17:17898200-17918000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr17:17898200-17918000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr17:17898400-17910000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr17:17898400-17911400	Weak transcription	HSMM	muscle
23	chr17:17898600-17908400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr17:17898600-17909800	Weak transcription	Adipose Nuclei	Adipose
25	chr17:17898600-17909800	Weak transcription	Ovary	ovary
26	chr17:17898600-17910600	Weak transcription	Placenta	Placenta
27	chr17:17898600-17910800	Weak transcription	Esophagus	oesophagus
28	chr17:17898600-17917600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr17:17898800-17908800	Weak transcription	NHEK	skin
30	chr17:17901200-17908200	Weak transcription	Fetal Stomach	stomach
31	chr17:17901200-17909200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr17:17903000-17911400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr17:17903200-17909800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr17:17903400-17909600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr17:17903400-17909800	Weak transcription	Liver	Liver
36	chr17:17903600-17908800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr17:17903600-17913200	Weak transcription	Gastric	stomach
38	chr17:17903600-17913600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr17:17903800-17909800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr17:17904000-17910000	Weak transcription	Fetal Intestine Large	intestine
41	chr17:17904000-17911800	Weak transcription	HepG2	liver
42	chr17:17905000-17910800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr17:17905000-17912000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr17:17905800-17909600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr17:17905800-17909800	Weak transcription	Thymus	Thymus
46	chr17:17905800-17911400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr17:17906000-17908200	Weak transcription	Primary T cells from cord blood	blood
48	chr17:17906000-17911800	Weak transcription	NHDF-Ad	bronchial
49	chr17:17906000-17912000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr17:17906000-17914800	Weak transcription	Rectal Mucosa Donor 31	rectum

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