Variant report

Variant	rs10005706
Chromosome Location	chr4:99481685-99481686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:99481670-99481709	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr4:99481546-99481886	H1-hESC	embryonic stem cell:	n/a	chr4:99481654-99481664
3	RAD21	chr4:99481537-99481815	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr4:99481509-99481841	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr4:99481613-99481693	Medullo	brain:	n/a	n/a
6	CTCF	chr4:99481523-99481702	GM12878	blood:	n/a	n/a
7	GATA3	chr4:99481596-99481885	T-47D	breast:	n/a	n/a
8	MAX	chr4:99481550-99481824	H1-hESC	embryonic stem cell:	n/a	chr4:99481654-99481664
9	CTCF	chr4:99481615-99481695	K562	blood:	n/a	n/a

Variant related genes	Relation type
TSPAN5	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10000857	0.97[EUR][1000 genomes]
rs10001528	1.00[EUR][1000 genomes]
rs10007752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10010485	0.90[EUR][1000 genomes]
rs10029528	1.00[CEU][hapmap]
rs10030396	1.00[CEU][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs10031904	1.00[CEU][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes]
rs10032578	1.00[CEU][hapmap]
rs12644470	0.86[JPT][hapmap]
rs17027682	1.00[CEU][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs17027707	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17027758	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17027760	1.00[CEU][hapmap]
rs17027826	1.00[CEU][hapmap]
rs17027841	1.00[CEU][hapmap]
rs17027845	1.00[CEU][hapmap]
rs17027851	1.00[CEU][hapmap]
rs1919212	0.90[EUR][1000 genomes]
rs28372028	0.86[EUR][1000 genomes]
rs28445981	1.00[EUR][1000 genomes]
rs28502504	0.90[EUR][1000 genomes]
rs28504661	0.90[EUR][1000 genomes]
rs28532945	0.86[EUR][1000 genomes]
rs28576181	0.97[EUR][1000 genomes]
rs28635613	0.97[EUR][1000 genomes]
rs28648419	0.90[EUR][1000 genomes]
rs28696298	0.86[EUR][1000 genomes]
rs28712025	0.90[EUR][1000 genomes]
rs28758777	0.90[EUR][1000 genomes]
rs72902292	0.90[EUR][1000 genomes]
rs9990571	0.90[EUR][1000 genomes]
rs9991086	0.90[EUR][1000 genomes]
rs9993039	1.00[EUR][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

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99466800-99501600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:99468400-99482200	Weak transcription	Esophagus	oesophagus
3	chr4:99469000-99482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:99475200-99482400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr4:99475400-99482000	Enhancers	Brain Cingulate Gyrus	brain
6	chr4:99475400-99482200	Enhancers	Brain Angular Gyrus	brain
7	chr4:99475800-99482200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr4:99476000-99482200	Enhancers	Fetal Brain Female	brain
9	chr4:99477200-99482800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:99477400-99486800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:99477400-99487600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:99477400-99487600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:99477800-99482800	Weak transcription	HMEC	breast
14	chr4:99478000-99483000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:99478200-99481800	Enhancers	Brain Anterior Caudate	brain
16	chr4:99478600-99481800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:99478600-99482200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:99478800-99482200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:99479000-99486800	Weak transcription	Fetal Lung	lung
20	chr4:99479000-99490200	Weak transcription	HSMMtube	muscle
21	chr4:99479000-99506400	Weak transcription	Aorta	Aorta
22	chr4:99479200-99482200	Weak transcription	NHEK	skin
23	chr4:99479200-99482400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr4:99479200-99482400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:99479200-99482800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:99479200-99484400	Weak transcription	HUVEC	blood vessel
27	chr4:99479200-99486800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:99479200-99486800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:99479200-99487000	Weak transcription	NH-A	brain
30	chr4:99479200-99487200	Weak transcription	NHLF	lung
31	chr4:99479600-99482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:99479800-99485800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:99479800-99486800	Weak transcription	Spleen	Spleen
34	chr4:99479800-99487000	Weak transcription	NHDF-Ad	bronchial
35	chr4:99480000-99481800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr4:99480000-99486800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:99480200-99486000	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:99480200-99486000	Weak transcription	Ovary	ovary
39	chr4:99480200-99486000	Weak transcription	Thymus	Thymus
40	chr4:99480400-99481800	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr4:99480400-99481800	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr4:99480400-99482200	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr4:99480400-99486800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr4:99480400-99487200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr4:99480600-99486200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr4:99480800-99481800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:99481200-99481800	Enhancers	HSMM	muscle
48	chr4:99481200-99485600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr4:99481200-99486800	Weak transcription	Brain Germinal Matrix	brain
50	chr4:99481400-99482800	Weak transcription	Fetal Heart	heart

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