Variant report

Variant	rs1399990
Chromosome Location	chr2:190041761-190041762
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	chr2:190041672..190043788-chr2:190044467..190046580,2	MCF-7	breast:
2	chr2:190036925..190039844-chr2:190040601..190043479,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204262	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10190073	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10210890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10211173	1.00[AMR][1000 genomes]
rs10931399	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12693529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13014478	0.95[AFR][1000 genomes]
rs1515863	1.00[AMR][1000 genomes]
rs1519180	1.00[AMR][1000 genomes]
rs1818585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2037170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2037171	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34556340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34606082	1.00[AMR][1000 genomes]
rs3914569	1.00[AMR][1000 genomes]
rs57449412	1.00[AMR][1000 genomes]
rs57484527	1.00[AMR][1000 genomes]
rs58082189	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58624621	1.00[AMR][1000 genomes]
rs59784139	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61325916	1.00[AMR][1000 genomes]
rs61621835	1.00[AMR][1000 genomes]
rs6434329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6434331	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6434332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6434333	1.00[AMR][1000 genomes]
rs6434336	1.00[AMR][1000 genomes]
rs6706066	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73978807	1.00[AMR][1000 genomes]
rs73978813	1.00[AMR][1000 genomes]
rs73978814	1.00[AMR][1000 genomes]
rs73978816	1.00[AMR][1000 genomes]
rs73978826	1.00[AMR][1000 genomes]
rs73978829	1.00[AMR][1000 genomes]
rs73981483	1.00[AMR][1000 genomes]
rs7578627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7594988	1.00[AMR][1000 genomes]
rs7606163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs939156	1.00[AMR][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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190029400-190042200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:190029600-190043400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:190029800-190043200	Weak transcription	Psoas Muscle	Psoas
4	chr2:190030400-190043400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:190034000-190043400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:190037400-190042600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:190037400-190042600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:190039800-190044800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:190040200-190044800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:190040400-190045000	Active TSS	Rectal Smooth Muscle	rectum
11	chr2:190040400-190045200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:190040600-190041800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:190040600-190044800	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr2:190040600-190045200	Active TSS	Fetal Muscle Leg	muscle
15	chr2:190040800-190042200	Transcr. at gene 5' and 3'	HSMM	muscle
16	chr2:190040800-190042400	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr2:190040800-190044800	Active TSS	NH-A	brain
18	chr2:190040800-190045000	Active TSS	Fetal Muscle Trunk	muscle
19	chr2:190040800-190045000	Active TSS	Right Atrium	heart
20	chr2:190040800-190045200	Active TSS	Aorta	Aorta
21	chr2:190040800-190045200	Active TSS	NHLF	lung
22	chr2:190041000-190042400	Enhancers	Liver	Liver
23	chr2:190041000-190042600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:190041000-190044800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:190041000-190044800	Active TSS	Duodenum Mucosa	Duodenum
26	chr2:190041000-190045000	Active TSS	Fetal Kidney	kidney
27	chr2:190041000-190045000	Active TSS	HSMMtube	muscle
28	chr2:190041200-190042000	Active TSS	HUVEC	blood vessel
29	chr2:190041200-190042600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:190041200-190044000	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr2:190041200-190044200	Active TSS	Fetal Intestine Small	intestine
32	chr2:190041200-190044800	Active TSS	Muscle Satellite Cultured Cells	--
33	chr2:190041200-190045000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:190041200-190045400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:190041200-190045400	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr2:190041400-190042000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:190041400-190042200	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr2:190041400-190042200	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr2:190041400-190042600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:190041400-190044800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:190041400-190044800	Active TSS	Colon Smooth Muscle	Colon
42	chr2:190041400-190045000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:190041400-190045000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:190041400-190045000	Active TSS	Adipose Nuclei	Adipose
45	chr2:190041400-190045000	Active TSS	Fetal Lung	lung
46	chr2:190041400-190045000	Active TSS	NHDF-Ad	bronchial
47	chr2:190041400-190045200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:190041400-190045200	Active TSS	Fetal Stomach	stomach
49	chr2:190041600-190041800	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr2:190041600-190042400	Weak transcription	Right Ventricle	heart

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