Variant report

Variant	rs12792781
Chromosome Location	chr11:57060562-57060563
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57059403..57062089-chr11:57076689..57079376,2	MCF-7	breast:
2	chr11:57059679..57063275-chr11:57091400..57095134,4	MCF-7	breast:
3	chr11:57059068..57062878-chr11:57064900..57069732,5	K562	blood:
4	chr11:57058210..57060578-chr11:57077243..57079019,2	MCF-7	breast:
5	chr11:57059815..57061654-chr11:57084021..57086891,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254662	Chromatin interaction
ENSG00000149115	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10792083	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs10896595	0.92[ASN][1000 genomes]
rs10896597	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10896599	0.89[ASN][1000 genomes]
rs11228968	0.95[ASN][1000 genomes]
rs11228975	0.95[ASN][1000 genomes]
rs11228976	0.95[ASN][1000 genomes]
rs11228978	0.95[ASN][1000 genomes]
rs11228980	0.95[ASN][1000 genomes]
rs11228982	0.88[ASN][1000 genomes]
rs11228984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11228985	0.98[ASN][1000 genomes]
rs11600878	0.89[ASN][1000 genomes]
rs11604560	0.95[ASN][1000 genomes]
rs11604778	0.84[ASN][1000 genomes]
rs11605053	0.98[ASN][1000 genomes]
rs11607817	0.95[ASN][1000 genomes]
rs12419065	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12421633	0.95[ASN][1000 genomes]
rs12421755	0.95[ASN][1000 genomes]
rs12797769	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17572970	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17651610	0.95[ASN][1000 genomes]
rs17652078	0.95[ASN][1000 genomes]
rs1892963	0.95[ASN][1000 genomes]
rs1892964	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1939489	0.98[ASN][1000 genomes]
rs1939495	0.95[ASN][1000 genomes]
rs2155230	0.95[ASN][1000 genomes]
rs2155231	0.87[ASN][1000 genomes]
rs2226613	0.99[ASN][1000 genomes]
rs2276038	0.82[JPT][hapmap]
rs2511026	0.83[ASN][1000 genomes]
rs2511029	0.87[ASN][1000 genomes]
rs2511030	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2846042	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2846050	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2846051	0.85[ASN][1000 genomes]
rs2851722	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35610294	0.93[ASN][1000 genomes]
rs3935068	0.96[ASN][1000 genomes]
rs4384399	0.95[ASN][1000 genomes]
rs4565915	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479949	0.92[ASN][1000 genomes]
rs4938855	0.95[ASN][1000 genomes]
rs4938857	0.95[ASN][1000 genomes]
rs4938859	0.94[ASN][1000 genomes]
rs4938861	0.95[ASN][1000 genomes]
rs4939132	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.99[ASN][1000 genomes]
rs499318	0.91[ASN][1000 genomes]
rs5012051	0.81[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs519277	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs522656	0.87[ASN][1000 genomes]
rs528101	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58295319	0.91[ASN][1000 genomes]
rs590240	0.87[ASN][1000 genomes]
rs599947	0.87[ASN][1000 genomes]
rs625565	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs652016	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs654635	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6591413	0.95[ASN][1000 genomes]
rs6591415	0.95[ASN][1000 genomes]
rs6591416	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591417	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102963	0.95[ASN][1000 genomes]
rs7120644	0.95[ASN][1000 genomes]
rs7128371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130252	0.95[ASN][1000 genomes]
rs72921992	0.97[ASN][1000 genomes]
rs7935236	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12792781	OR4C6	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57046000-57062000	Weak transcription	Right Atrium	heart
2	chr11:57051800-57062000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:57052400-57078200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:57055200-57063400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:57056800-57062200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:57056800-57064200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr11:57056800-57065400	Weak transcription	Fetal Heart	heart
8	chr11:57057000-57060600	Weak transcription	Pancreas	Pancrea
9	chr11:57057000-57060800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr11:57057000-57061800	Weak transcription	Fetal Stomach	stomach
11	chr11:57057000-57062000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:57057000-57062200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:57057000-57064800	Weak transcription	Spleen	Spleen
14	chr11:57057000-57065200	Weak transcription	Brain Hippocampus Middle	brain
15	chr11:57057000-57066400	Weak transcription	Colonic Mucosa	Colon
16	chr11:57057000-57066800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:57057200-57060600	Weak transcription	Adipose Nuclei	Adipose
18	chr11:57057200-57060600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr11:57057200-57060800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:57057200-57061000	Weak transcription	Lung	lung
21	chr11:57057200-57061800	Weak transcription	Fetal Lung	lung
22	chr11:57057200-57062000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr11:57057200-57062000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr11:57057200-57062400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr11:57057200-57065000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:57057200-57065200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr11:57057200-57066400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:57057200-57066800	Weak transcription	Brain Substantia Nigra	brain
29	chr11:57057400-57061800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr11:57057400-57061800	Weak transcription	Brain Anterior Caudate	brain
31	chr11:57057400-57062000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr11:57057400-57062000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr11:57057400-57063800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr11:57057400-57064400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr11:57057400-57065800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr11:57057400-57066600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr11:57057800-57061800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr11:57057800-57064200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:57057800-57064800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:57057800-57065600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:57057800-57066400	Weak transcription	Fetal Kidney	kidney
42	chr11:57058200-57060800	Weak transcription	NHDF-Ad	bronchial
43	chr11:57058200-57062200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr11:57058200-57066600	Weak transcription	HUVEC	blood vessel
45	chr11:57058400-57060600	Weak transcription	Fetal Intestine Large	intestine
46	chr11:57058400-57060600	Weak transcription	Fetal Intestine Small	intestine
47	chr11:57058400-57065000	Weak transcription	NHLF	lung
48	chr11:57058600-57060600	Weak transcription	Gastric	stomach
49	chr11:57058600-57060800	Weak transcription	Small Intestine	intestine
50	chr11:57058800-57062800	Enhancers	Liver	Liver

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