Variant report

Variant	rs4938861
Chromosome Location	chr11:57056050-57056051
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57053497..57056158-chr11:57061828..57064102,2	K562	blood:
2	chr11:57054342..57056926-chr11:57058891..57060493,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10501367	0.82[GIH][hapmap]
rs10792083	0.96[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs10792085	0.84[CEU][hapmap]
rs10896595	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896597	0.89[ASN][1000 genomes]
rs10896599	0.86[ASN][1000 genomes]
rs10896602	0.84[CEU][hapmap]
rs11228968	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11228975	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11228976	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11228978	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11228980	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11228982	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11228984	0.83[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs11228985	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11228988	0.87[EUR][1000 genomes]
rs11544374	0.82[GIH][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs11600878	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11604373	0.83[EUR][1000 genomes]
rs11604560	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11604778	0.84[ASN][1000 genomes]
rs11605053	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11607817	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12419065	0.94[ASN][1000 genomes]
rs12421633	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12421755	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12792781	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.95[ASN][1000 genomes]
rs12797769	0.96[ASN][1000 genomes]
rs17572970	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17651610	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17652078	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1892963	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1892964	0.89[ASN][1000 genomes]
rs1939489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1939495	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2155230	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2155231	0.84[ASN][1000 genomes]
rs2226613	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276038	0.82[JPT][hapmap]
rs2511026	0.85[ASN][1000 genomes]
rs2511029	0.84[ASN][1000 genomes]
rs2511030	0.89[ASN][1000 genomes]
rs2846042	0.89[ASN][1000 genomes]
rs2846049	0.83[ASN][1000 genomes]
rs2846050	0.89[ASN][1000 genomes]
rs2846051	0.82[ASN][1000 genomes]
rs2851722	0.89[ASN][1000 genomes]
rs35610294	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3935068	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4384399	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4565915	0.95[ASN][1000 genomes]
rs479949	0.89[ASN][1000 genomes]
rs4938855	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4938857	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4938859	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4939132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs499318	0.88[ASN][1000 genomes]
rs5012051	0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs519277	0.89[ASN][1000 genomes]
rs522656	0.84[ASN][1000 genomes]
rs528101	0.89[ASN][1000 genomes]
rs58295319	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs590240	0.84[ASN][1000 genomes]
rs599947	0.84[ASN][1000 genomes]
rs625565	0.89[ASN][1000 genomes]
rs652016	0.86[ASN][1000 genomes]
rs654635	0.89[ASN][1000 genomes]
rs6591408	0.82[YRI][hapmap]
rs6591413	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6591415	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6591416	0.95[ASN][1000 genomes]
rs6591417	0.95[ASN][1000 genomes]
rs7102963	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7119375	0.82[GIH][hapmap]
rs7120644	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7128371	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7130252	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72921992	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7935236	0.91[ASN][1000 genomes]
rs7943761	0.83[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4938861	OR5T1	cis	cerebellum	SCAN
rs4938861	OR4C6	cis	parietal	SCAN
rs4938861	OR5AN1	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57046000-57062000	Weak transcription	Right Atrium	heart
2	chr11:57048200-57056400	Weak transcription	Gastric	stomach
3	chr11:57051400-57056200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:57051600-57056200	Weak transcription	Stomach Mucosa	stomach
5	chr11:57051600-57056600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr11:57051800-57056200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:57051800-57056400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:57051800-57056400	Weak transcription	Esophagus	oesophagus
9	chr11:57051800-57062000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:57052000-57056200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:57052000-57056200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr11:57052000-57056400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:57052000-57056600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:57052200-57056400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr11:57052200-57056400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:57052200-57060400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:57052400-57057200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:57052400-57078200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr11:57053800-57056400	Weak transcription	Placenta	Placenta
20	chr11:57055000-57056400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:57055000-57058400	Enhancers	HMEC	breast
22	chr11:57055200-57056200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr11:57055200-57056600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr11:57055200-57058400	Enhancers	NHEK	skin
25	chr11:57055200-57063400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:57055400-57057000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:57055400-57057400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:57055400-57057800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:57055400-57057800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr11:57055400-57058200	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr11:57055400-57058400	Enhancers	Fetal Intestine Large	intestine
32	chr11:57055600-57056400	Enhancers	HSMM	muscle
33	chr11:57055600-57057000	Enhancers	Colonic Mucosa	Colon
34	chr11:57055600-57058200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:57055600-57058200	Enhancers	NHDF-Ad	bronchial
36	chr11:57055600-57058400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr11:57055600-57058400	Enhancers	NH-A	brain
38	chr11:57055600-57058400	Enhancers	NHLF	lung
39	chr11:57055800-57056200	Enhancers	Small Intestine	intestine
40	chr11:57055800-57056200	Bivalent Enhancer	HepG2	liver
41	chr11:57055800-57056800	Enhancers	HSMMtube	muscle
42	chr11:57055800-57057400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:57055800-57057800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr11:57055800-57058200	Enhancers	HUVEC	blood vessel
45	chr11:57055800-57058400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr11:57055800-57058400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:57055800-57058400	Enhancers	Duodenum Mucosa	Duodenum
48	chr11:57056000-57056200	Flanking Active TSS	Osteobl	bone
49	chr11:57056000-57056400	Enhancers	Liver	Liver
50	chr11:57056000-57056600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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