Variant report

Variant	rs4699650
Chromosome Location	chr4:99466330-99466331
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99459317..99461488-chr4:99464335..99467316,2	K562	blood:
2	chr4:99463140..99464695-chr4:99465921..99468144,2	K562	blood:
3	chr4:99465722..99468319-chr4:99566226..99568875,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10018825	0.89[JPT][hapmap]
rs10021296	0.89[JPT][hapmap]
rs11097621	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11730384	0.87[CEU][hapmap];0.94[JPT][hapmap]
rs13114571	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13132635	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13134231	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13149070	0.89[JPT][hapmap]
rs17191936	0.80[CHB][hapmap]
rs17192060	0.83[CHB][hapmap]
rs1919211	0.92[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2866017	0.89[JPT][hapmap]
rs4699345	0.92[CEU][hapmap]
rs4699346	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699651	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699652	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6532742	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6532744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532745	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6532747	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6532748	0.96[CEU][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6827510	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6831464	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6831643	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6837359	0.94[JPT][hapmap]
rs6846287	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6854339	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7672134	0.89[JPT][hapmap]
rs7695093	0.83[CHB][hapmap]

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	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2760882	chr4:99460485-99521345	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4699650	TSPAN5	cis	cerebellum	SCAN
rs4699650	H2AFZ	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99446000-99467400	Weak transcription	Fetal Stomach	stomach
2	chr4:99449800-99467400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:99450200-99467400	Weak transcription	Osteobl	bone
4	chr4:99450800-99468000	Weak transcription	HSMM	muscle
5	chr4:99459000-99468000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:99459200-99468000	Weak transcription	Esophagus	oesophagus
7	chr4:99459200-99479600	Weak transcription	Spleen	Spleen
8	chr4:99459600-99467800	Weak transcription	NHLF	lung
9	chr4:99461000-99467400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:99463400-99467600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:99463600-99467600	Weak transcription	HMEC	breast
12	chr4:99463800-99478800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:99464000-99468000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:99464800-99467800	Enhancers	Fetal Brain Female	brain
15	chr4:99464800-99468000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:99465000-99466400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:99465000-99468400	Enhancers	Fetal Brain Male	brain
18	chr4:99465200-99466400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:99465200-99466400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:99465200-99466800	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr4:99465400-99466400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:99465400-99466400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:99465400-99466400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr4:99465400-99466400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr4:99465400-99466400	Enhancers	Brain Hippocampus Middle	brain
26	chr4:99465400-99466400	Enhancers	Fetal Muscle Leg	muscle
27	chr4:99465400-99466400	Enhancers	Thymus	Thymus
28	chr4:99465400-99466600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr4:99465400-99466600	Enhancers	Fetal Thymus	thymus
30	chr4:99465400-99466800	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr4:99465400-99466800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:99465400-99466800	Enhancers	Brain Substantia Nigra	brain
33	chr4:99465400-99467000	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr4:99465400-99467600	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr4:99465400-99467800	Enhancers	Brain Angular Gyrus	brain
36	chr4:99465400-99467800	Enhancers	Fetal Lung	lung
37	chr4:99465600-99466400	Enhancers	Primary T cells fromperipheralblood	blood
38	chr4:99465600-99466400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr4:99465600-99466400	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr4:99465600-99466400	Enhancers	Brain Germinal Matrix	brain
41	chr4:99465600-99466800	Enhancers	HUVEC	blood vessel
42	chr4:99465800-99467400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:99465800-99467400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:99465800-99467800	Weak transcription	Aorta	Aorta
45	chr4:99466000-99467400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr4:99466200-99466400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:99466200-99466600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:99466200-99467400	Weak transcription	Brain Anterior Caudate	brain
49	chr4:99466200-99467400	Weak transcription	Ovary	ovary
50	chr4:99466200-99467400	Weak transcription	NHDF-Ad	bronchial

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