Variant report

Variant	rs6487924
Chromosome Location	chr12:30785218-30785219
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	chr12:29503193..29506083-chr12:30783016..30785826,2	MCF-7	breast:
2	chr12:30784879..30786858-chr12:30788783..30790332,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133704	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10743725	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843791	0.80[AMR][1000 genomes]
rs10843794	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10843805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11050958	0.80[AMR][1000 genomes]
rs11051006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11051009	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11051023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11051026	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11051030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11051034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11051044	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11051046	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs11610452	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12306961	0.82[ASN][1000 genomes]
rs12308822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12310942	0.82[ASN][1000 genomes]
rs12315407	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12315446	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12371883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12372023	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2099028	0.82[ASN][1000 genomes]
rs3888018	0.86[GIH][hapmap];1.00[MEX][hapmap]
rs3906774	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56003450	0.97[ASN][1000 genomes]
rs56705455	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57153590	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59483134	0.91[ASN][1000 genomes]
rs6487929	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6487931	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7135005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7302606	0.96[EUR][1000 genomes]
rs7302757	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7303665	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7306125	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7307432	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7308638	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7310127	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7315859	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73292874	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74083892	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7955626	0.92[AMR][1000 genomes]
rs7963438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7963524	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7968669	0.82[ASN][1000 genomes]
rs7968760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972061	0.92[AMR][1000 genomes]
rs7974251	0.89[EUR][1000 genomes]
rs9651844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[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	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6487924	IPO8	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30767000-30785600	Weak transcription	Pancreas	Pancrea
2	chr12:30767000-30844200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:30771000-30812200	Weak transcription	Aorta	Aorta
4	chr12:30771200-30804200	Weak transcription	Fetal Brain Male	brain
5	chr12:30774600-30812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:30775600-30815400	Weak transcription	Right Ventricle	heart
7	chr12:30775800-30813200	Weak transcription	HMEC	breast
8	chr12:30775800-30815200	Weak transcription	NHEK	skin
9	chr12:30776000-30808400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr12:30776800-30791000	Weak transcription	Psoas Muscle	Psoas
11	chr12:30778000-30786400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:30779200-30812200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:30779400-30796400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:30779800-30825000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:30780200-30795000	Weak transcription	Fetal Intestine Small	intestine
16	chr12:30780400-30796200	Weak transcription	Hela-S3	cervix
17	chr12:30780600-30785800	Strong transcription	Stomach Smooth Muscle	stomach
18	chr12:30780600-30788400	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:30780800-30786000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:30780800-30786000	Strong transcription	Fetal Muscle Leg	muscle
21	chr12:30780800-30786200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:30780800-30792600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:30780800-30793000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:30780800-30793000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:30780800-30793200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr12:30780800-30793200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr12:30780800-30847000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:30781000-30787200	Strong transcription	Fetal Intestine Large	intestine
29	chr12:30781000-30792800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:30781000-30792800	Strong transcription	Primary T cells from cord blood	blood
31	chr12:30781000-30793000	Strong transcription	Liver	Liver
32	chr12:30781200-30786000	Strong transcription	Left Ventricle	heart
33	chr12:30781200-30786400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:30781200-30786800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:30781200-30787200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:30781200-30787200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:30781200-30787200	Strong transcription	Rectal Smooth Muscle	rectum
38	chr12:30781200-30787200	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:30781200-30790000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:30781200-30790200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr12:30781200-30792800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:30781200-30792800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr12:30781200-30792800	Strong transcription	Adipose Nuclei	Adipose
44	chr12:30781200-30792800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr12:30781200-30793000	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr12:30781200-30793000	Strong transcription	Fetal Thymus	thymus
47	chr12:30781200-30793200	Strong transcription	Dnd41	blood
48	chr12:30781200-30797600	Strong transcription	Primary B cells from cord blood	blood
49	chr12:30781200-30806600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr12:30781400-30786000	Strong transcription	Fetal Muscle Trunk	muscle

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