Variant report

Variant	rs7705824
Chromosome Location	chr5:96005617-96005618
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95985902..95988959-chr5:96004331..96007887,4	K562	blood:
2	chr5:95987307..95988959-chr5:96004331..96007033,2	K562	blood:
3	chr5:95996033..95999839-chr5:96004051..96008299,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10045215	0.88[ASN][1000 genomes]
rs10067766	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10075736	0.88[ASN][1000 genomes]
rs1421911	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs149319	0.81[GIH][hapmap];0.87[MKK][hapmap]
rs151835	1.00[JPT][hapmap]
rs151904	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs152005	0.90[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs152014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs152017	0.82[JPT][hapmap]
rs152020	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2351245	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs246109	0.81[ASN][1000 genomes]
rs26482	0.94[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs26483	0.88[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs26484	0.90[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs26485	1.00[CEU][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs26503	1.00[JPT][hapmap]
rs26504	1.00[JPT][hapmap]
rs28040	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28093	0.86[JPT][hapmap]
rs28104	0.86[JPT][hapmap]
rs31248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs31249	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs31250	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4267886	0.86[ASN][1000 genomes]
rs4590196	0.94[ASW][hapmap];0.94[CEU][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6556937	0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6860934	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6897588	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7704167	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7733671	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7705824	CAST	cis	lung	GTEx
rs7705824	CAST	cis	Adipose Subcutaneous	GTEx
rs7705824	CTC-506B8.1	cis	Nerve Tibial	GTEx
rs7705824	CAST	Cis_1M	lymphoblastoid	RTeQTL
rs7705824	CAST	cis	Nerve Tibial	GTEx
rs7705824	CTC-506B8.1	cis	Whole Blood	GTEx
rs7705824	CAST	cis	parietal	SCAN
rs7705824	CAST	cis	Whole Blood	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95999400-96018200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:95999400-96038000	Weak transcription	Fetal Stomach	stomach
3	chr5:95999600-96006800	Weak transcription	Right Ventricle	heart
4	chr5:95999600-96006800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:95999600-96006800	Weak transcription	Spleen	Spleen
6	chr5:95999600-96012400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:95999600-96016600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:95999600-96016600	Weak transcription	HSMMtube	muscle
9	chr5:95999600-96026000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:95999600-96028200	Weak transcription	Aorta	Aorta
11	chr5:95999600-96037800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:95999600-96038000	Weak transcription	Fetal Lung	lung
13	chr5:95999800-96010800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr5:95999800-96022800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr5:95999800-96024600	Weak transcription	Fetal Heart	heart
16	chr5:96000400-96007600	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr5:96000400-96010800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:96000400-96013400	Weak transcription	Placenta	Placenta
19	chr5:96000400-96016400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:96000400-96018400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:96000600-96010800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:96000600-96011000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr5:96000600-96013200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:96000800-96007000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:96000800-96010800	Weak transcription	Osteobl	bone
26	chr5:96000800-96011000	Weak transcription	HUVEC	blood vessel
27	chr5:96000800-96011800	Weak transcription	Primary T cells from cord blood	blood
28	chr5:96000800-96013000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:96000800-96016200	Weak transcription	NH-A	brain
30	chr5:96000800-96037600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr5:96001000-96007200	Enhancers	Stomach Mucosa	stomach
32	chr5:96001000-96011000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr5:96001000-96011000	Weak transcription	HMEC	breast
34	chr5:96001200-96011600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr5:96001400-96010800	Weak transcription	NHDF-Ad	bronchial
36	chr5:96001400-96013000	Weak transcription	NHEK	skin
37	chr5:96001400-96013200	Weak transcription	HSMM	muscle
38	chr5:96001600-96037000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr5:96002000-96007600	Enhancers	Fetal Intestine Large	intestine
40	chr5:96002200-96011000	Weak transcription	NHLF	lung
41	chr5:96002400-96006600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:96002400-96007000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:96002400-96010800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr5:96002400-96012800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr5:96002400-96018400	Weak transcription	Psoas Muscle	Psoas
46	chr5:96002400-96027800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr5:96002400-96037600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr5:96002400-96038200	Weak transcription	Esophagus	oesophagus
49	chr5:96002600-96010800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr5:96003000-96009200	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links