Variant report

Variant	rs7214799
Chromosome Location	chr17:45702099-45702100
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45700634..45703555-chr17:45708176..45711349,3	MCF-7	breast:
2	chr17:45700978..45703641-chr17:45726585..45728583,2	K562	blood:
3	chr17:45694884..45697521-chr17:45701270..45704059,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108424	Chromatin interaction
ENSG00000141279	Chromatin interaction
ENSG00000263766	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10163469	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10853090	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11079782	0.88[ASN][1000 genomes]
rs11079783	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11079784	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1138193	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11650372	0.81[EUR][1000 genomes]
rs11656855	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11656856	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11870935	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs11871606	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12150231	0.81[EUR][1000 genomes]
rs12936468	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12937560	0.84[ASN][1000 genomes]
rs12943464	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1912486	0.82[CEU][hapmap]
rs1912487	0.93[CEU][hapmap]
rs1962307	0.85[ASW][hapmap];0.92[CEU][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2013383	0.81[CEU][hapmap]
rs2317826	0.83[TSI][hapmap]
rs34200664	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35919601	0.86[ASN][1000 genomes]
rs3760370	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3760371	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3809868	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs3865314	0.89[ASN][1000 genomes]
rs4092460	0.90[ASN][1000 genomes]
rs4239162	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.94[ASN][1000 genomes]
rs4239163	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4289035	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4399567	0.95[ASN][1000 genomes]
rs4497739	0.92[CEU][hapmap];0.94[YRI][hapmap]
rs4793836	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4793842	0.93[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.96[ASN][1000 genomes]
rs4793908	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4793913	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4793978	0.81[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4794001	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4794047	0.93[CEU][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs4794048	0.83[TSI][hapmap]
rs4794052	0.81[CEU][hapmap]
rs4794053	0.81[CEU][hapmap]
rs4794058	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[TSI][hapmap]
rs55633793	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56226803	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62074015	0.92[ASN][1000 genomes]
rs6503796	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6503804	0.81[CEU][hapmap]
rs6503807	0.81[CEU][hapmap]
rs6505048	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6505049	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6505062	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7207542	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7210738	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs7213086	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7219303	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7220935	0.82[EUR][1000 genomes]
rs7222225	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7223029	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73315878	0.93[ASN][1000 genomes]
rs8065437	0.81[EUR][1000 genomes]
rs8065669	0.83[TSI][hapmap]
rs8070463	0.86[CHD][hapmap]
rs8072644	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs8075411	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8075566	0.81[CEU][hapmap]
rs8078309	0.81[CEU][hapmap]
rs8078880	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8082284	0.82[ASN][1000 genomes]
rs9635762	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9635763	0.85[ASN][1000 genomes]
rs9891111	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9893901	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs9905581	0.85[CEU][hapmap]
rs9905922	0.97[ASN][1000 genomes]
rs9912311	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv516872	chr17:45419139-45702280	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv525267	chr17:45451894-45735706	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv1811231	chr17:45520374-45764956	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv1813964	chr17:45520374-45764956	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv2758458	chr17:45520374-45764956	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	esv2758693	chr17:45520374-45764956	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv428344	chr17:45520374-45764956	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs7214799	VPS25	cis	cerebellum	SCAN
rs7214799	LOC653479	cis	multi-tissue	Pritchard
rs7214799	TBKBP1	cis	Nerve Tibial	GTEx
rs7214799	HOXB6	cis	cerebellum	SCAN
rs7214799	CDK5RAP3	cis	cerebellum	SCAN
rs7214799	C17orf57	cis	parietal	SCAN
rs7214799	TBKBP1	cis	lymphoblastoid	seeQTL
rs7214799	TBKBP1	cis	multi-tissue	Pritchard
rs7214799	TBKBP1	cis	Artery Tibial	GTEx
rs7214799	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx
rs7214799	C17orf57	cis	cerebellum	SCAN
rs7214799	MRPL45P2	cis	lymphoblastoid	seeQTL
rs7214799	KLHL11	cis	cerebellum	SCAN
rs7214799	TBKBP1	cis	lung	GTEx
rs7214799	MRPL45P2	cis	Muscle Skeletal	GTEx
rs7214799	KRTAP9-3	cis	cerebellum	SCAN
rs7214799	TBKBP1	cis	Artery Aorta	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45663800-45702800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr17:45667400-45718200	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr17:45670000-45703000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr17:45672400-45704200	Strong transcription	Fetal Muscle Trunk	muscle
5	chr17:45672600-45703000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr17:45686800-45703400	Strong transcription	Fetal Stomach	stomach
7	chr17:45688800-45702400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr17:45688800-45702400	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr17:45688800-45703000	Strong transcription	Placenta	Placenta
10	chr17:45689000-45703000	Strong transcription	Fetal Thymus	thymus
11	chr17:45689200-45707800	Weak transcription	Gastric	stomach
12	chr17:45691800-45716600	Weak transcription	Right Ventricle	heart
13	chr17:45692800-45714600	Weak transcription	Aorta	Aorta
14	chr17:45694600-45702600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr17:45694600-45702600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr17:45694600-45702800	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr17:45695400-45704000	Strong transcription	GM12878-XiMat	blood
18	chr17:45696600-45709200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr17:45696600-45713600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr17:45696600-45726000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr17:45696800-45707200	Weak transcription	Ovary	ovary
22	chr17:45696800-45726200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:45697000-45725800	Weak transcription	Brain Substantia Nigra	brain
24	chr17:45697200-45703600	Weak transcription	Fetal Brain Male	brain
25	chr17:45697200-45713400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr17:45697200-45713600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr17:45697200-45726000	Weak transcription	Brain Angular Gyrus	brain
28	chr17:45698000-45716000	Weak transcription	Psoas Muscle	Psoas
29	chr17:45698600-45714400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr17:45698800-45702600	Weak transcription	Colonic Mucosa	Colon
31	chr17:45698800-45702800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr17:45699400-45702200	Strong transcription	Adipose Nuclei	Adipose
33	chr17:45699400-45702400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr17:45699400-45707200	Weak transcription	Pancreas	Pancrea
35	chr17:45699400-45707200	Weak transcription	Right Atrium	heart
36	chr17:45699400-45726000	Weak transcription	Brain Anterior Caudate	brain
37	chr17:45699400-45726200	Weak transcription	Fetal Kidney	kidney
38	chr17:45699600-45702600	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr17:45699600-45713800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr17:45699800-45702400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr17:45699800-45702600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr17:45699800-45707200	Weak transcription	Stomach Mucosa	stomach
43	chr17:45699800-45707800	Weak transcription	K562	blood
44	chr17:45699800-45712600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr17:45699800-45713400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr17:45699800-45717600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr17:45700000-45703000	Weak transcription	Hela-S3	cervix
48	chr17:45700000-45704200	Strong transcription	Fetal Muscle Leg	muscle
49	chr17:45700000-45707200	Weak transcription	Fetal Lung	lung
50	chr17:45700000-45710000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links