Variant report

Variant	rs11169658
Chromosome Location	chr12:51393824-51393825
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51393339..51395355-chr12:51418733..51421410,2	MCF-7	breast:
2	chr12:51384221..51386732-chr12:51393559..51396729,3	MCF-7	breast:
3	chr12:51389653..51392226-chr12:51393368..51395789,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10876122	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876133	0.84[CHB][hapmap]
rs10876135	0.83[CHB][hapmap]
rs11169625	1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169629	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169634	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169640	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169643	1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169651	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169662	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169675	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169681	0.80[EUR][1000 genomes]
rs11169696	0.83[CHB][hapmap]
rs11169706	0.84[CHB][hapmap]
rs11169708	0.83[CHB][hapmap]
rs12227734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230388	0.84[CHB][hapmap]
rs12424460	0.84[CHB][hapmap]
rs17125371	0.81[CHB][hapmap]
rs1982777	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2016533	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2239860	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269682	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269683	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2359189	0.83[CHB][hapmap]
rs2436636	0.84[CHB][hapmap]
rs2452794	0.84[CHB][hapmap]
rs2452795	0.83[CHB][hapmap]
rs2640518	0.83[CHB][hapmap]
rs2640525	0.83[CHB][hapmap]
rs2730659	0.84[CHB][hapmap]
rs2956427	0.84[CHB][hapmap]
rs3809320	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768871	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768953	0.83[CHB][hapmap]
rs4768957	0.83[CHB][hapmap]
rs7295893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7399214	0.83[CHB][hapmap]
rs8490	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51378000-51401800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr12:51378600-51399000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:51378800-51396000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:51379400-51396000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:51379400-51396200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:51379600-51395600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:51379800-51394600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:51379800-51396400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:51380000-51396200	Strong transcription	Dnd41	blood
10	chr12:51380200-51396400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:51380200-51396600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:51380200-51401800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr12:51380200-51402200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr12:51380400-51396200	Strong transcription	Fetal Brain Female	brain
15	chr12:51380400-51396200	Strong transcription	Placenta	Placenta
16	chr12:51380600-51399600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:51381200-51395800	Strong transcription	Primary B cells from peripheral blood	blood
18	chr12:51381200-51402200	Strong transcription	Fetal Thymus	thymus
19	chr12:51381200-51402200	Weak transcription	Psoas Muscle	Psoas
20	chr12:51381200-51402400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:51381200-51403000	Strong transcription	Fetal Muscle Leg	muscle
22	chr12:51381400-51394200	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:51381400-51396400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr12:51381400-51403000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:51381800-51401600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr12:51381800-51401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:51381800-51402400	Strong transcription	Liver	Liver
28	chr12:51382000-51394600	Strong transcription	Lung	lung
29	chr12:51382000-51395800	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:51382000-51396400	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:51382000-51402000	Strong transcription	Fetal Stomach	stomach
32	chr12:51382000-51402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:51382400-51399400	Strong transcription	Fetal Intestine Large	intestine
34	chr12:51382600-51399400	Strong transcription	Fetal Intestine Small	intestine
35	chr12:51384000-51394600	Strong transcription	HepG2	liver
36	chr12:51385600-51402600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:51386000-51406600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:51386000-51414200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr12:51386200-51398800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:51386800-51402200	Weak transcription	Right Atrium	heart
41	chr12:51387000-51396200	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr12:51387800-51394000	Strong transcription	Osteobl	bone
43	chr12:51388000-51395800	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:51388000-51401000	Strong transcription	Primary T cells from cord blood	blood
45	chr12:51388200-51394200	Strong transcription	Primary hematopoietic stem cells	blood
46	chr12:51388200-51394200	Strong transcription	A549	lung
47	chr12:51388200-51396200	Strong transcription	Brain Substantia Nigra	brain
48	chr12:51388200-51396200	Strong transcription	Stomach Smooth Muscle	stomach
49	chr12:51388200-51402000	Strong transcription	Adipose Nuclei	Adipose
50	chr12:51388400-51394400	Strong transcription	Aorta	Aorta

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