Variant report

Variant	rs7733671
Chromosome Location	chr5:96000269-96000270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95995785..95997823-chr5:95999172..96000986,2	K562	blood:
2	chr5:96000243..96001872-chr5:96034533..96037143,2	MCF-7	breast:
3	chr5:96000044..96002037-chr5:96005700..96007687,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10045215	0.92[ASN][1000 genomes]
rs10067766	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10075736	0.92[ASN][1000 genomes]
rs1421911	0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs149319	0.81[GIH][hapmap];0.89[MKK][hapmap]
rs151835	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs151904	1.00[JPT][hapmap]
rs152005	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs152014	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs152017	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs152020	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2351245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs26482	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs26483	0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs26484	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs26485	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs26503	1.00[JPT][hapmap]
rs26504	1.00[JPT][hapmap]
rs28040	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28093	0.86[JPT][hapmap]
rs28104	0.86[JPT][hapmap]
rs31248	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs31249	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs31250	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4267886	0.84[ASN][1000 genomes]
rs4590196	0.87[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6556937	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6860934	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6897588	1.00[CEU][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7704167	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7705824	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7733671	CAST	Cis_1M	lymphoblastoid	RTeQTL
rs7733671	CAST	cis	Thyroid	GTEx
rs7733671	CTC-506B8.1	cis	Whole Blood	GTEx
rs7733671	CAST	cis	Nerve Tibial	GTEx
rs7733671	CAST	cis	multi-tissue	Pritchard
rs7733671	CAST	cis	lung	GTEx
rs7733671	CAST	cis	parietal	SCAN
rs7733671	CTC-506B8.1	cis	lung	GTEx
rs7733671	CAST	cis	Adipose Subcutaneous	GTEx
rs7733671	CAST	cis	Whole Blood	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95997200-96000800	Active TSS	Stomach Mucosa	stomach
2	chr5:95999400-96000600	Enhancers	HepG2	liver
3	chr5:95999400-96000800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr5:95999400-96001000	Flanking Active TSS	HMEC	breast
5	chr5:95999400-96001400	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr5:95999400-96001600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr5:95999400-96002000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:95999400-96002600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:95999400-96002800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:95999400-96005000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr5:95999400-96018200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr5:95999400-96038000	Weak transcription	Fetal Stomach	stomach
13	chr5:95999600-96000400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr5:95999600-96000400	Enhancers	Primary B cells from cord blood	blood
15	chr5:95999600-96000400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:95999600-96000400	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:95999600-96000400	Enhancers	Pancreas	Pancrea
18	chr5:95999600-96000400	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr5:95999600-96000800	Enhancers	Primary T cells from cord blood	blood
20	chr5:95999600-96000800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr5:95999600-96000800	Enhancers	Liver	Liver
22	chr5:95999600-96000800	Enhancers	HUVEC	blood vessel
23	chr5:95999600-96000800	Enhancers	Osteobl	bone
24	chr5:95999600-96001000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr5:95999600-96001200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr5:95999600-96001400	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr5:95999600-96001400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr5:95999600-96001400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:95999600-96001800	Weak transcription	Small Intestine	intestine
30	chr5:95999600-96001800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr5:95999600-96002000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:95999600-96002000	Weak transcription	Colonic Mucosa	Colon
33	chr5:95999600-96002000	Weak transcription	Psoas Muscle	Psoas
34	chr5:95999600-96002200	Weak transcription	Esophagus	oesophagus
35	chr5:95999600-96003800	Weak transcription	Fetal Kidney	kidney
36	chr5:95999600-96003800	Weak transcription	Gastric	stomach
37	chr5:95999600-96004400	Weak transcription	Right Atrium	heart
38	chr5:95999600-96004600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:95999600-96004600	Weak transcription	Lung	lung
40	chr5:95999600-96004600	Weak transcription	Ovary	ovary
41	chr5:95999600-96006800	Weak transcription	Right Ventricle	heart
42	chr5:95999600-96006800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr5:95999600-96006800	Weak transcription	Spleen	Spleen
44	chr5:95999600-96012400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr5:95999600-96016600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr5:95999600-96016600	Weak transcription	HSMMtube	muscle
47	chr5:95999600-96026000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:95999600-96028200	Weak transcription	Aorta	Aorta
49	chr5:95999600-96037800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:95999600-96038000	Weak transcription	Fetal Lung	lung

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