Variant report

Variant	rs1989379
Chromosome Location	chr17:19631420-19631421
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:19482050..19483613-chr17:19630992..19632977,2	MCF-7	breast:
2	chr17:19625321..19633420-chr17:19643892..19652817,11	MCF-7	breast:
3	chr17:19624830..19631833-chr17:19654160..19660410,12	MCF-7	breast:
4	chr17:19618336..19623572-chr17:19629964..19633338,7	MCF-7	breast:
5	chr17:19627403..19631543-chr17:19639531..19642900,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228983	Chromatin interaction
ENSG00000180638	Chromatin interaction
ENSG00000262681	Chromatin interaction
ENSG00000264785	Chromatin interaction
ENSG00000108602	Chromatin interaction
ENSG00000230607	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1006553	0.88[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs1006556	0.90[CHB][hapmap]
rs1042183	0.86[GIH][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs11650088	0.88[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs11651480	0.94[EUR][1000 genomes]
rs11653719	0.91[EUR][1000 genomes]
rs11655457	0.93[EUR][1000 genomes]
rs11657205	0.80[TSI][hapmap]
rs12945000	0.92[EUR][1000 genomes]
rs12948881	0.86[GIH][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs17720157	0.96[EUR][1000 genomes]
rs2016823	0.91[EUR][1000 genomes]
rs2072329	0.86[GIH][hapmap];0.81[EUR][1000 genomes]
rs2072330	0.89[EUR][1000 genomes]
rs2228100	0.87[CHB][hapmap]
rs3760486	0.84[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs3760487	0.84[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs3786036	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3826507	0.88[EUR][1000 genomes]
rs4646785	0.82[CHB][hapmap]

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	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv907866	chr17:19582533-19697976	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv1807724	chr17:19597423-19656009	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv907867	chr17:19603060-19697976	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	esv1793043	chr17:19604821-19670329	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv526290	chr17:19613357-19651482	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv457704	chr17:19620477-19663747	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv470582	chr17:19620477-19663747	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv574580	chr17:19620477-19663747	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1989379	COPS3	cis	cerebellum	SCAN
rs1989379	FLJ10847	cis	multi-tissue	Pritchard
rs1989379	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19617600-19635400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr17:19623200-19648400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:19628200-19640800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr17:19629200-19633800	Enhancers	Fetal Muscle Leg	muscle
5	chr17:19629400-19632000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr17:19629400-19632200	Enhancers	Colon Smooth Muscle	Colon
7	chr17:19629800-19632200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr17:19629800-19632200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr17:19629800-19632200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr17:19629800-19633200	Enhancers	Brain Substantia Nigra	brain
11	chr17:19630000-19632200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr17:19630000-19632200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr17:19630000-19632200	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr17:19630000-19632200	Enhancers	HMEC	breast
15	chr17:19630000-19632200	Enhancers	NHDF-Ad	bronchial
16	chr17:19630000-19633400	Enhancers	HSMMtube	muscle
17	chr17:19630200-19631600	Enhancers	Right Ventricle	heart
18	chr17:19630200-19631800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr17:19630200-19632000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr17:19630200-19632000	Enhancers	Osteobl	bone
21	chr17:19630200-19632200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr17:19630200-19632200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr17:19630200-19632200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr17:19630200-19632200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr17:19630200-19632200	Enhancers	NHEK	skin
26	chr17:19630200-19632400	Enhancers	Right Atrium	heart
27	chr17:19630200-19632400	Enhancers	A549	lung
28	chr17:19630200-19632800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr17:19630200-19632800	Enhancers	Brain Angular Gyrus	brain
30	chr17:19630200-19633600	Enhancers	Ovary	ovary
31	chr17:19630400-19631800	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr17:19630400-19632000	Enhancers	Spleen	Spleen
33	chr17:19630400-19632200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr17:19630400-19632200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr17:19630400-19632200	Enhancers	Liver	Liver
36	chr17:19630400-19632200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr17:19630400-19632200	Enhancers	Fetal Lung	lung
38	chr17:19630400-19632200	Enhancers	Pancreas	Pancrea
39	chr17:19630600-19631800	Enhancers	Duodenum Mucosa	Duodenum
40	chr17:19630600-19632000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr17:19630600-19632000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr17:19630600-19632000	Enhancers	NHLF	lung
43	chr17:19630600-19632200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr17:19630600-19632200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr17:19630600-19632200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr17:19630600-19632200	Enhancers	Esophagus	oesophagus
47	chr17:19630600-19632200	Enhancers	Fetal Intestine Small	intestine
48	chr17:19630600-19632200	Enhancers	Fetal Stomach	stomach
49	chr17:19630600-19632200	Enhancers	Left Ventricle	heart
50	chr17:19630600-19632200	Enhancers	Small Intestine	intestine

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