Variant report

Variant	rs11612531
Chromosome Location	chr12:45806979-45806980
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	chr12:45806466..45809321-chr12:46119882..46122422,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273015	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10506261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10506262	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880779	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880781	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10880782	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10880783	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11183000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11183001	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11183004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11183009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11183012	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11183019	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11183027	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11183028	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11183030	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11183034	0.94[EUR][1000 genomes]
rs11183040	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11536237	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11611476	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11612092	0.90[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12230667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12231032	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12314896	0.95[JPT][hapmap]
rs12578337	0.84[YRI][hapmap]
rs12578593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12580984	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580991	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12809717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812732	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12813734	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12819619	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12829496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1316280	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17095868	0.81[AMR][1000 genomes]
rs17095871	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17095872	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2081589	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2081590	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2408260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34031195	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34470081	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34785109	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35634751	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35754392	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35816444	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3803176	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57911796	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58503970	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59893450	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6582546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7299836	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302251	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7304126	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7308092	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7313617	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7965912	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7968063	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7977798	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9788195	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9788251	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr12:45744800-45809200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:45752200-45809200	Weak transcription	Small Intestine	intestine
3	chr12:45759200-45822600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:45764400-45821000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:45764600-45815400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:45772600-45815400	Weak transcription	K562	blood
7	chr12:45774800-45811400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:45780400-45829800	Weak transcription	Brain Anterior Caudate	brain
9	chr12:45783200-45818800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:45783400-45826400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:45786200-45809200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:45786600-45827000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:45792000-45828600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr12:45792600-45822600	Weak transcription	Colonic Mucosa	Colon
15	chr12:45792600-45827000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:45792800-45811800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:45793000-45827600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr12:45794200-45807400	Strong transcription	A549	lung
19	chr12:45794200-45823200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr12:45794400-45807400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:45794600-45809200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:45794600-45812200	Weak transcription	Fetal Brain Male	brain
23	chr12:45794800-45807600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:45795000-45812200	Weak transcription	Fetal Brain Female	brain
25	chr12:45795200-45808000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:45795200-45813200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:45795200-45817800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:45795400-45813400	Strong transcription	Dnd41	blood
29	chr12:45795600-45807000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr12:45795600-45807600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:45795600-45825600	Strong transcription	Fetal Intestine Large	intestine
32	chr12:45795800-45808200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:45796000-45807400	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr12:45796000-45812400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:45796400-45812200	Weak transcription	Hela-S3	cervix
36	chr12:45796400-45829600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:45796600-45808000	Strong transcription	GM12878-XiMat	blood
38	chr12:45796600-45828400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr12:45796600-45828600	Weak transcription	Brain Substantia Nigra	brain
40	chr12:45796600-45828800	Weak transcription	Brain Angular Gyrus	brain
41	chr12:45797600-45819200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:45799800-45807200	Strong transcription	Primary hematopoietic stem cells	blood
43	chr12:45799800-45807600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr12:45799800-45808000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr12:45799800-45811800	Strong transcription	Fetal Stomach	stomach
46	chr12:45800400-45807000	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr12:45800800-45813000	Strong transcription	Primary T cells from cord blood	blood
48	chr12:45801000-45807600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr12:45801200-45808200	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:45801400-45808600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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