Variant report

Variant	rs11901914
Chromosome Location	chr2:190028489-190028490
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190027832..190030639-chr2:190032693..190035632,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10165127	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10165257	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1016622	0.95[EUR][1000 genomes]
rs10166385	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10167242	0.83[ASN][1000 genomes]
rs10172607	0.94[ASN][1000 genomes]
rs10173224	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10184895	0.94[ASN][1000 genomes]
rs10755002	0.93[ASN][1000 genomes]
rs10931401	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10931403	0.93[ASN][1000 genomes]
rs10931405	0.88[ASN][1000 genomes]
rs10931411	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12474942	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12618316	0.95[EUR][1000 genomes]
rs12621657	0.85[ASN][1000 genomes]
rs12999125	0.92[ASN][1000 genomes]
rs13005714	0.95[EUR][1000 genomes]
rs13005834	0.95[EUR][1000 genomes]
rs13006065	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13013089	0.95[EUR][1000 genomes]
rs13015183	0.93[ASN][1000 genomes]
rs13020999	0.95[EUR][1000 genomes]
rs13024858	0.89[EUR][1000 genomes]
rs13028226	0.92[ASN][1000 genomes]
rs13030984	0.92[EUR][1000 genomes]
rs13031609	0.81[ASN][1000 genomes]
rs13408928	0.96[ASN][1000 genomes]
rs13411992	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs13413518	0.96[ASN][1000 genomes]
rs1356161	0.92[ASN][1000 genomes]
rs1356166	0.93[ASN][1000 genomes]
rs1464135	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474000	0.85[ASN][1000 genomes]
rs1515864	0.92[EUR][1000 genomes]
rs1515866	0.93[ASN][1000 genomes]
rs1515869	0.92[EUR][1000 genomes]
rs1533618	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1546617	0.93[ASN][1000 genomes]
rs1913892	0.92[ASN][1000 genomes]
rs1949327	0.89[EUR][1000 genomes]
rs1973666	0.90[ASN][1000 genomes]
rs1983318	0.93[ASN][1000 genomes]
rs2138373	0.89[EUR][1000 genomes]
rs2351631	0.93[ASN][1000 genomes]
rs2351632	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2351633	0.93[ASN][1000 genomes]
rs2351635	0.86[ASN][1000 genomes]
rs36019389	0.94[EUR][1000 genomes]
rs4417749	0.92[EUR][1000 genomes]
rs4667263	0.92[EUR][1000 genomes]
rs4667266	0.95[EUR][1000 genomes]
rs4667268	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4667270	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4667271	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4667275	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62182417	0.86[EUR][1000 genomes]
rs6434324	0.89[EUR][1000 genomes]
rs6434325	0.92[EUR][1000 genomes]
rs6434334	0.87[ASN][1000 genomes]
rs6434337	0.88[ASN][1000 genomes]
rs6704568	0.86[ASN][1000 genomes]
rs6728877	0.92[ASN][1000 genomes]
rs6732534	0.91[ASN][1000 genomes]
rs6741804	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6749559	0.83[EUR][1000 genomes]
rs6752781	0.95[EUR][1000 genomes]
rs6761868	0.86[ASN][1000 genomes]
rs7560973	0.89[EUR][1000 genomes]
rs7574281	0.87[ASN][1000 genomes]
rs7593860	0.92[EUR][1000 genomes]
rs7599222	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7603704	0.91[ASN][1000 genomes]
rs7606337	0.92[EUR][1000 genomes]
rs9288163	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs939158	0.86[ASN][1000 genomes]
rs939160	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11901914	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190017600-190028800	Weak transcription	Fetal Muscle Leg	muscle
2	chr2:190018800-190029600	Weak transcription	Ovary	ovary
3	chr2:190019600-190040000	Weak transcription	Fetal Intestine Small	intestine
4	chr2:190021000-190031400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:190026200-190028600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:190026200-190028800	Genic enhancers	HSMM	muscle
7	chr2:190026400-190029000	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr2:190026600-190029000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:190026600-190029200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr2:190026600-190029600	Enhancers	HSMMtube	muscle
11	chr2:190026600-190030200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr2:190026600-190032000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr2:190026800-190029200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr2:190026800-190029800	Enhancers	Rectal Smooth Muscle	rectum
15	chr2:190026800-190030800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:190027000-190029000	Enhancers	Colon Smooth Muscle	Colon
17	chr2:190027000-190029400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr2:190027200-190028800	Weak transcription	Liver	Liver
19	chr2:190027200-190030800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:190027400-190029200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr2:190027600-190029800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:190027600-190032000	Enhancers	Fetal Lung	lung
23	chr2:190027800-190029200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr2:190027800-190029400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:190027800-190031400	Enhancers	NH-A	brain
26	chr2:190028000-190029400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:190028000-190029600	Enhancers	Fetal Heart	heart
28	chr2:190028000-190030800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:190028000-190032800	Enhancers	NHLF	lung
30	chr2:190028200-190028600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:190028200-190029000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr2:190028200-190029000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:190028200-190029000	Flanking Active TSS	Osteobl	bone
34	chr2:190028200-190029200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr2:190028200-190030000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:190028200-190030400	Enhancers	Hela-S3	cervix
37	chr2:190028200-190030600	Enhancers	Adipose Nuclei	Adipose
38	chr2:190028400-190028600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:190028400-190028600	Flanking Active TSS	NHDF-Ad	bronchial
40	chr2:190028400-190028800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr2:190028400-190028800	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:190028400-190029000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:190028400-190029000	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr2:190028400-190029000	Enhancers	Brain Germinal Matrix	brain
45	chr2:190028400-190029000	Enhancers	Stomach Smooth Muscle	stomach
46	chr2:190028400-190029200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:190028400-190029200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:190028400-190029200	Flanking Active TSS	A549	lung
49	chr2:190028400-190029400	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr2:190028400-190029400	Enhancers	Fetal Kidney	kidney

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