Variant report

Variant	rs17616603
Chromosome Location	chr17:45959620-45959621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45928046..45933138-chr17:45958246..45966286,8	K562	blood:
2	chr17:45957419..45959674-chr17:45964404..45967485,3	K562	blood:
3	chr17:45958143..45959731-chr17:45960109..45961631,2	MCF-7	breast:
4	chr17:45923661..45925474-chr17:45958248..45959760,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP6-1	chr17:45956838-45959764	ENSG00000266821.1

Variant related genes	Relation type
ENSG00000189120	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1108833	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11654010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11870852	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13353189	0.88[ASN][1000 genomes]
rs2325747	0.82[ASN][1000 genomes]
rs2325749	0.81[AMR][1000 genomes]
rs34064155	0.87[ASN][1000 genomes]
rs35336840	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794261	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4794286	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7211859	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17616603	SKAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45954600-45964400	Enhancers	Fetal Intestine Large	intestine
2	chr17:45956400-45961600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:45956400-45961800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr17:45956400-45962400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr17:45956600-45961200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr17:45956600-45961800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr17:45956600-45961800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:45956600-45962000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr17:45956800-45960400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr17:45956800-45961800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr17:45957600-45959800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr17:45957600-45964200	Enhancers	Fetal Intestine Small	intestine
13	chr17:45958000-45962200	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr17:45958200-45964400	Enhancers	Placenta	Placenta
15	chr17:45958400-45963000	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr17:45958600-45961800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:45959000-45961400	Enhancers	Lung	lung
18	chr17:45959000-45963600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr17:45959200-45959800	Enhancers	HSMM	muscle
20	chr17:45959200-45960000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr17:45959200-45960000	Enhancers	HUVEC	blood vessel
22	chr17:45959200-45960200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr17:45959200-45960400	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr17:45959200-45961000	Enhancers	Right Ventricle	heart
25	chr17:45959200-45961200	Enhancers	Spleen	Spleen
26	chr17:45959200-45963800	Enhancers	Fetal Thymus	thymus
27	chr17:45959400-45959800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr17:45959400-45959800	Enhancers	Primary hematopoietic stem cells	blood
29	chr17:45959400-45959800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr17:45959400-45959800	Enhancers	Small Intestine	intestine
31	chr17:45959400-45960000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr17:45959400-45960000	Active TSS	Rectal Smooth Muscle	rectum
33	chr17:45959400-45960200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr17:45959400-45960200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr17:45959400-45960200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr17:45959400-45960200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr17:45959400-45960200	Flanking Active TSS	NHDF-Ad	bronchial
38	chr17:45959400-45960200	Flanking Active TSS	Osteobl	bone
39	chr17:45959400-45962200	Enhancers	Fetal Kidney	kidney
40	chr17:45959400-45963400	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr17:45959600-45959800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
42	chr17:45959600-45959800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
43	chr17:45959600-45959800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr17:45959600-45959800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
45	chr17:45959600-45959800	Enhancers	Hela-S3	cervix
46	chr17:45959600-45959800	Enhancers	NHLF	lung
47	chr17:45959600-45960000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr17:45959600-45960000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr17:45959600-45960000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
50	chr17:45959600-45960000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin

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