Variant report

Variant	rs11112289
Chromosome Location	chr12:105389068-105389069
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	chr12:105378452..105381595-chr12:105388431..105392391,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151131	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10507189	0.91[CEU][hapmap];0.81[AMR][1000 genomes]
rs10861279	0.91[CEU][hapmap]
rs10861283	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10861284	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10861285	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10861289	0.91[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10861290	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10861298	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11112211	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs11112213	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs11112214	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11112216	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11112219	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11112222	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11112226	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11112236	0.81[AMR][1000 genomes]
rs11112239	0.82[ASN][1000 genomes]
rs11112240	0.82[ASN][1000 genomes]
rs11112244	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11112247	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11112255	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11112262	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112267	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11112273	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112274	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11112275	0.93[EUR][1000 genomes]
rs11112278	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112282	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112288	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112290	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112298	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112300	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112301	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112302	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112304	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112305	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112312	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112317	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112326	0.87[AMR][1000 genomes]
rs11112344	1.00[JPT][hapmap]
rs11519610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11519721	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368856	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12371663	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12372030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12372069	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12372636	0.84[AMR][1000 genomes]
rs16891	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2047128	0.91[CEU][hapmap];0.90[JPT][hapmap]
rs4331189	1.00[CEU][hapmap]
rs4405400	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs56741182	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7303811	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9943769	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv869	chr12:105363425-105394904	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105381600-105392400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:105381600-105392400	Weak transcription	Stomach Mucosa	stomach
3	chr12:105381800-105389200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr12:105381800-105392400	Weak transcription	Right Atrium	heart
5	chr12:105381800-105392800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:105381800-105392800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:105381800-105393600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:105381800-105398000	Strong transcription	A549	lung
9	chr12:105381800-105407400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:105381800-105411400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:105382000-105390800	Strong transcription	Fetal Muscle Leg	muscle
12	chr12:105382000-105392000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:105382000-105394600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:105382000-105397800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:105382000-105401400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:105382000-105401400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr12:105382200-105390000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:105382200-105392200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:105382200-105392800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:105382200-105395000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:105382200-105395200	Strong transcription	Primary B cells from cord blood	blood
22	chr12:105382200-105395600	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr12:105382200-105401400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:105382200-105402000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:105382200-105402000	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:105382200-105402000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:105382200-105402600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:105382400-105401200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:105382400-105401400	Strong transcription	Liver	Liver
30	chr12:105382600-105389400	Strong transcription	HSMM	muscle
31	chr12:105382600-105391000	Strong transcription	Fetal Lung	lung
32	chr12:105382600-105397800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:105382800-105390800	Strong transcription	Fetal Thymus	thymus
34	chr12:105382800-105394600	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:105382800-105394800	Strong transcription	Primary T cells from cord blood	blood
36	chr12:105382800-105398000	Strong transcription	Adipose Nuclei	Adipose
37	chr12:105383000-105390800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr12:105383000-105391200	Strong transcription	HMEC	breast
39	chr12:105383000-105402000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:105383200-105390600	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:105383200-105391800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr12:105383200-105392800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr12:105383200-105396400	Strong transcription	Fetal Intestine Large	intestine
44	chr12:105383200-105398000	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr12:105383400-105393200	Strong transcription	Dnd41	blood
46	chr12:105383400-105394200	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr12:105383400-105399000	Strong transcription	Primary B cells from peripheral blood	blood
48	chr12:105383600-105389800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:105383600-105392600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:105383600-105394800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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