Variant report

Variant	rs1399991
Chromosome Location	chr2:190028496-190028497
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	chr2:190027832..190030639-chr2:190032693..190035632,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1016622	0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs10931400	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10931401	0.81[JPT][hapmap]
rs10931404	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11681286	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11691604	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12104769	0.95[EUR][1000 genomes]
rs12105389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12611950	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12615823	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12618438	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12621035	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12621806	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12621939	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12991770	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12993719	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12995956	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12999122	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12999125	0.82[AFR][1000 genomes]
rs12999996	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13004722	0.84[EUR][1000 genomes]
rs13005652	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13005821	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13005834	0.80[AFR][1000 genomes]
rs13011374	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13011485	0.85[EUR][1000 genomes]
rs13012327	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13012649	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13015283	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13016231	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13017413	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13019076	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13021508	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13022633	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13028967	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13029705	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13031211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13031549	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13033421	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1356162	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1356163	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1356164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1356165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1356166	0.80[AFR][1000 genomes]
rs1356167	1.00[CEU][hapmap];0.81[JPT][hapmap];0.97[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1356168	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1399992	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1464135	0.81[JPT][hapmap]
rs1515874	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1515876	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1546617	0.82[AFR][1000 genomes]
rs1568334	0.85[EUR][1000 genomes]
rs1878085	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1949484	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1965422	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2138374	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2222256	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2351627	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2351636	0.84[EUR][1000 genomes]
rs35475196	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35772309	0.94[ASN][1000 genomes]
rs3914778	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233801	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4428040	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4667264	1.00[CEU][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4667265	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4667266	0.86[YRI][hapmap]
rs4667268	0.84[AFR][1000 genomes]
rs4667272	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4667274	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4667276	0.85[EUR][1000 genomes]
rs4667277	0.85[EUR][1000 genomes]
rs4998559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60124911	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62182416	0.91[EUR][1000 genomes]
rs6434339	0.89[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs6708419	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6714088	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6719104	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6728877	0.83[AFR][1000 genomes]
rs6737071	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7419888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7561002	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7564611	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7576165	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7587147	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7587956	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7607133	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7609495	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];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

No data

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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