Variant report

Variant	rs4699345
Chromosome Location	chr4:99466506-99466507
allele	C/T
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: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10002696	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10006366	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10006430	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10018825	0.95[CHB][hapmap]
rs10021296	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs10025051	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11097619	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11730384	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs13108940	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13123700	0.92[ASN][1000 genomes]
rs13134231	0.88[CEU][hapmap]
rs13149070	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs1528547	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1534554	0.84[ASN][1000 genomes]
rs1534555	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1573478	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs1919210	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1919211	0.92[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs2037832	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2866016	0.94[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs2866017	0.95[CHB][hapmap]
rs28886705	0.86[ASN][1000 genomes]
rs4447870	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4699343	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4699344	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4699348	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4699349	0.93[JPT][hapmap]
rs4699354	0.94[JPT][hapmap]
rs4699639	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4699640	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4699644	0.81[CEU][hapmap];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4699646	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699648	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699650	0.92[CEU][hapmap]
rs6532748	0.96[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs6532751	0.89[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs6815038	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6823547	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847124	0.87[ASN][1000 genomes]
rs71600251	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7672134	0.95[CHB][hapmap];0.90[CHD][hapmap]
rs7678323	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs9760870	0.85[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4699345	BMPR1B	cis	cerebellum	SCAN
rs4699345	TSPAN5	cis	cerebellum	SCAN
rs4699345	DAPP1	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

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	chr4:99465000-99468400	Enhancers	Fetal Brain Male	brain
17	chr4:99465200-99466800	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr4:99465400-99466600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr4:99465400-99466600	Enhancers	Fetal Thymus	thymus
20	chr4:99465400-99466800	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr4:99465400-99466800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr4:99465400-99466800	Enhancers	Brain Substantia Nigra	brain
23	chr4:99465400-99467000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr4:99465400-99467600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr4:99465400-99467800	Enhancers	Brain Angular Gyrus	brain
26	chr4:99465400-99467800	Enhancers	Fetal Lung	lung
27	chr4:99465600-99466800	Enhancers	HUVEC	blood vessel
28	chr4:99465800-99467400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:99465800-99467400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:99465800-99467800	Weak transcription	Aorta	Aorta
31	chr4:99466000-99467400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr4:99466200-99466600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:99466200-99467400	Weak transcription	Brain Anterior Caudate	brain
34	chr4:99466200-99467400	Weak transcription	Ovary	ovary
35	chr4:99466200-99467400	Weak transcription	NHDF-Ad	bronchial
36	chr4:99466200-99467800	Weak transcription	Fetal Heart	heart
37	chr4:99466400-99467200	Weak transcription	Brain Germinal Matrix	brain
38	chr4:99466400-99467400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:99466400-99467400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr4:99466400-99467400	Weak transcription	Brain Hippocampus Middle	brain
41	chr4:99466400-99467400	Weak transcription	Fetal Muscle Leg	muscle
42	chr4:99466400-99467800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:99466400-99467800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:99466400-99468000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:99466400-99468000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:99466400-99477000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links