Variant report

Variant	rs12948299
Chromosome Location	chr17:45403057-45403058
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	chr17:45399600..45403116-chr17:45404916..45409576,7	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC040934.1-2	chr17:45402274-45403111	NONHSAT054297

Variant related genes	Relation type
ENSG00000178852	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11079772	0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11651643	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[YRI][hapmap]
rs11658426	0.82[EUR][1000 genomes]
rs12451744	0.82[ASN][1000 genomes]
rs12600865	0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1912484	0.89[CEU][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1912486	0.88[CEU][hapmap];0.86[YRI][hapmap]
rs1969267	0.80[ASN][1000 genomes]
rs2136749	0.84[AMR][1000 genomes]
rs2136750	0.81[AMR][1000 genomes]
rs2271803	0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2292346	0.80[AMR][1000 genomes]
rs34589418	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35161461	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35435669	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35983484	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3736438	1.00[ASW][hapmap];0.89[CEU][hapmap];0.87[YRI][hapmap]
rs3760372	0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs3809865	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3826536	0.88[CEU][hapmap];0.82[YRI][hapmap]
rs3851808	1.00[ASW][hapmap];0.83[LWK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4968257	0.88[CEU][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4968314	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4968316	0.80[EUR][1000 genomes]
rs4968318	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[LWK][hapmap];0.82[MKK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6504836	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7216112	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7218813	0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7221224	0.84[AMR][1000 genomes]
rs7221232	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8075058	1.00[ASW][hapmap];0.89[CEU][hapmap];0.87[YRI][hapmap]
rs8075410	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8075843	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[LWK][hapmap];0.82[MKK][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs8079142	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[MKK][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9303534	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9893410	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9894594	0.82[AMR][1000 genomes]
rs9905073	0.81[AMR][1000 genomes]
rs9915222	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv962445	chr17:45397004-45428018	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12948299	KRT13	cis	parietal	SCAN
rs12948299	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx
rs12948299	C17orf57	cis	cerebellum	SCAN
rs12948299	MRPL45P2	cis	lymphoblastoid	seeQTL
rs12948299	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs12948299	HOXB2	cis	cerebellum	SCAN
rs12948299	DBF4B	cis	cerebellum	SCAN
rs12948299	TBKBP1	cis	Artery Tibial	GTEx
rs12948299	NBR1	cis	parietal	SCAN
rs12948299	VPS25	cis	cerebellum	SCAN
rs12948299	TBKBP1	cis	Nerve Tibial	GTEx
rs12948299	TBKBP1	cis	lung	GTEx
rs12948299	C17orf57	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45402000-45428600	Weak transcription	Spleen	Spleen
2	chr17:45402000-45442600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr17:45402200-45407000	Weak transcription	HepG2	liver
4	chr17:45402200-45416800	Weak transcription	Lung	lung
5	chr17:45402200-45420400	Weak transcription	Pancreas	Pancrea
6	chr17:45402200-45446400	Weak transcription	Colon Smooth Muscle	Colon
7	chr17:45402200-45500800	Weak transcription	Aorta	Aorta
8	chr17:45402400-45404000	Weak transcription	Fetal Muscle Leg	muscle
9	chr17:45402400-45405000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr17:45402400-45406200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr17:45402400-45408800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr17:45402400-45411000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr17:45402400-45412200	Weak transcription	Adipose Nuclei	Adipose
14	chr17:45402400-45412800	Weak transcription	Ovary	ovary
15	chr17:45402400-45416000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr17:45402400-45419400	Weak transcription	Liver	Liver
17	chr17:45402400-45419600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr17:45402400-45421200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr17:45402400-45421400	Weak transcription	Fetal Kidney	kidney
20	chr17:45402400-45421600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr17:45402400-45423400	Weak transcription	NHDF-Ad	bronchial
22	chr17:45402400-45424200	Weak transcription	Fetal Brain Male	brain
23	chr17:45402400-45427200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr17:45402400-45428400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr17:45402400-45433600	Weak transcription	Fetal Heart	heart
26	chr17:45402400-45433600	Weak transcription	Fetal Intestine Small	intestine
27	chr17:45402400-45433600	Weak transcription	Fetal Stomach	stomach
28	chr17:45402400-45435800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr17:45402400-45436000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr17:45402600-45416800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr17:45402600-45422200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr17:45402600-45423000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr17:45402600-45423400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr17:45402600-45424600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr17:45402600-45428800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr17:45402800-45403200	Enhancers	Primary B cells from peripheral blood	blood
37	chr17:45402800-45408800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr17:45402800-45409000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr17:45402800-45422400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr17:45402800-45440800	Weak transcription	Primary T cells from cord blood	blood
41	chr17:45403000-45408800	Weak transcription	Primary B cells from cord blood	blood
42	chr17:45403000-45413000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr17:45403000-45429400	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links