Variant report

Variant	rs16947228
Chromosome Location	chr12:117457541-117457542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:117447389..117449402-chr12:117456865..117458856,2	MCF-7	breast:
2	chr12:117455374..117458365-chr12:117461422..117463402,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11068269	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11829895	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11830219	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11832649	1.00[CEU][hapmap]
rs11835474	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1320027	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16947216	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16947235	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16947246	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35749640	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36021180	1.00[EUR][1000 genomes]
rs3935958	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs3956801	1.00[EUR][1000 genomes]
rs55693524	1.00[EUR][1000 genomes]
rs56103902	1.00[EUR][1000 genomes]
rs56721166	1.00[EUR][1000 genomes]
rs71469784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7313865	1.00[EUR][1000 genomes]
rs7964659	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7977227	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7980519	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs937567	1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs952934	1.00[CEU][hapmap];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	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv899541	chr12:117414974-117497066	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117387800-117463600	Weak transcription	HMEC	breast
2	chr12:117393800-117471000	Weak transcription	Small Intestine	intestine
3	chr12:117426200-117466600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:117443800-117461600	Weak transcription	Colonic Mucosa	Colon
5	chr12:117444000-117462800	Weak transcription	K562	blood
6	chr12:117448400-117462000	Weak transcription	Hela-S3	cervix
7	chr12:117450200-117461800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:117450400-117461800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:117450800-117461200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:117450800-117461600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:117452400-117460200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:117452400-117461800	Weak transcription	Brain Angular Gyrus	brain
13	chr12:117452400-117463400	Strong transcription	Fetal Intestine Large	intestine
14	chr12:117452400-117463800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr12:117452400-117469000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:117452600-117458000	Strong transcription	Adipose Nuclei	Adipose
17	chr12:117452600-117458000	Weak transcription	Fetal Heart	heart
18	chr12:117452600-117461200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:117452600-117463600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr12:117452800-117462400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr12:117452800-117463200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr12:117452800-117463200	Strong transcription	A549	lung
23	chr12:117452800-117465200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:117452800-117468400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr12:117452800-117470200	Weak transcription	HUVEC	blood vessel
26	chr12:117452800-117479000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:117453000-117459000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:117453200-117461600	Weak transcription	Brain Substantia Nigra	brain
29	chr12:117453200-117461800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:117453200-117461800	Weak transcription	Stomach Mucosa	stomach
31	chr12:117453200-117463600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:117453400-117457600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:117453400-117457600	Weak transcription	HepG2	liver
34	chr12:117453400-117461400	Weak transcription	Right Ventricle	heart
35	chr12:117453600-117457800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:117453600-117461600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:117453600-117461600	Weak transcription	Ovary	ovary
38	chr12:117453600-117461600	Weak transcription	Thymus	Thymus
39	chr12:117453600-117461800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr12:117453600-117462200	Weak transcription	NHLF	lung
41	chr12:117453600-117463200	Strong transcription	Fetal Muscle Leg	muscle
42	chr12:117453600-117470600	Weak transcription	Psoas Muscle	Psoas
43	chr12:117453800-117457800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:117453800-117461200	Weak transcription	Fetal Thymus	thymus
45	chr12:117453800-117461400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr12:117453800-117461600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:117453800-117461800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:117453800-117462000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:117454000-117458400	Weak transcription	Brain Anterior Caudate	brain
50	chr12:117454000-117459600	Weak transcription	Osteobl	bone

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