Variant report

Variant	rs12320880
Chromosome Location	chr12:105392220-105392221
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105378452..105381595-chr12:105388431..105392391,5	MCF-7	breast:
2	chr12:105384826..105387201-chr12:105391835..105393587,2	K562	blood:
3	chr12:105392063..105394759-chr12:105462525..105464694,2	K562	blood:
4	chr12:105379691..105382014-chr12:105391921..105394682,4	MCF-7	breast:
5	chr12:105391022..105393004-chr12:105396428..105398011,2	MCF-7	breast:
6	chr12:105391750..105393633-chr12:105396940..105398737,2	K562	blood:

Variant related genes	Relation type
ENSG00000151131	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10160991	0.80[ASN][1000 genomes]
rs10161522	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10507186	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10507187	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10507188	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11112218	1.00[CEU][hapmap]
rs11112276	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112277	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112279	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112283	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112303	0.91[EUR][1000 genomes]
rs11112307	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112346	1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap]
rs11503466	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12296144	0.97[EUR][1000 genomes]
rs12299385	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12299936	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12300005	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];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300010	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12301432	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];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12301850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12306191	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12306443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12306848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12308952	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12310790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313077	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12314995	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12315975	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12315983	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12316001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319632	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12320024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12320195	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12321224	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12321226	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12321381	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17036439	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17036463	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17036494	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17036505	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17036509	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17036534	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17036542	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17036549	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17036558	0.91[EUR][1000 genomes]
rs17041531	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs35879768	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3812795	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3935722	0.94[EUR][1000 genomes]
rs4077312	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4267155	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4268581	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4357778	0.94[EUR][1000 genomes]
rs4375513	1.00[CEU][hapmap]
rs4393405	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4451800	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4553438	1.00[CEU][hapmap]
rs58005679	0.94[EUR][1000 genomes]
rs58447363	0.94[EUR][1000 genomes]
rs58483223	0.91[EUR][1000 genomes]
rs60057011	0.85[EUR][1000 genomes]
rs60096703	0.91[EUR][1000 genomes]
rs60310033	0.85[EUR][1000 genomes]
rs60809012	0.85[EUR][1000 genomes]
rs60956548	0.94[EUR][1000 genomes]
rs61638859	0.91[EUR][1000 genomes]
rs7131977	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7299019	1.00[CEU][hapmap]
rs73387265	0.91[EUR][1000 genomes]
rs7964906	0.95[ASN][1000 genomes]
rs7970504	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9738733	0.91[EUR][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	chr12:105381800-105392400	Weak transcription	Right Atrium	heart
4	chr12:105381800-105392800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:105381800-105392800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:105381800-105393600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:105381800-105398000	Strong transcription	A549	lung
8	chr12:105381800-105407400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:105381800-105411400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:105382000-105394600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:105382000-105397800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:105382000-105401400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:105382000-105401400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:105382200-105392800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr12:105382200-105395000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:105382200-105395200	Strong transcription	Primary B cells from cord blood	blood
17	chr12:105382200-105395600	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr12:105382200-105401400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:105382200-105402000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr12:105382200-105402000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:105382200-105402000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:105382200-105402600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:105382400-105401200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:105382400-105401400	Strong transcription	Liver	Liver
25	chr12:105382600-105397800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:105382800-105394600	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr12:105382800-105394800	Strong transcription	Primary T cells from cord blood	blood
28	chr12:105382800-105398000	Strong transcription	Adipose Nuclei	Adipose
29	chr12:105383000-105402000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:105383200-105392800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr12:105383200-105396400	Strong transcription	Fetal Intestine Large	intestine
32	chr12:105383200-105398000	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr12:105383400-105393200	Strong transcription	Dnd41	blood
34	chr12:105383400-105394200	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr12:105383400-105399000	Strong transcription	Primary B cells from peripheral blood	blood
36	chr12:105383600-105392600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr12:105383600-105394800	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:105383600-105401600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:105383800-105393800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:105383800-105397800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:105383800-105401200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:105384000-105394200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:105384000-105395000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr12:105384000-105402000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:105384200-105394400	Strong transcription	Stomach Smooth Muscle	stomach
46	chr12:105384400-105392800	Strong transcription	Fetal Brain Female	brain
47	chr12:105384400-105394800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr12:105384800-105400000	Strong transcription	Brain Anterior Caudate	brain
49	chr12:105385000-105393800	Strong transcription	Placenta	Placenta
50	chr12:105385200-105394200	Strong transcription	Brain Hippocampus Middle	brain

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