Variant report

Variant	rs2180073
Chromosome Location	chr1:184524811-184524812
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1007224	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10797972	0.81[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs10797977	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10911606	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11588922	0.80[AMR][1000 genomes]
rs12125349	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12127674	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1339563	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1339564	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1339565	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1339566	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1339567	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1416752	0.92[CEU][hapmap]
rs1569842	0.87[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs1884200	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs2001270	0.81[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap]
rs2038307	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2038308	1.00[CEU][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2144294	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2180077	0.87[CHB][hapmap]
rs2890015	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4650667	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4651208	0.83[CHB][hapmap]
rs4651210	0.92[CEU][hapmap];0.87[CHB][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs4651211	0.84[EUR][1000 genomes]
rs4651213	0.89[CEU][hapmap]
rs4651217	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4651219	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6666704	0.80[EUR][1000 genomes]
rs7517518	0.80[EUR][1000 genomes]
rs7533466	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7544240	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9970984	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9970990	0.92[AMR][1000 genomes];0.90[EUR][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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184502600-184527200	Weak transcription	Fetal Brain Female	brain
2	chr1:184505800-184530800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:184505800-184531600	Weak transcription	Fetal Stomach	stomach
4	chr1:184511400-184530400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:184512200-184530200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:184512200-184543600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:184512400-184530200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:184514400-184543800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:184515200-184531200	Weak transcription	NHLF	lung
10	chr1:184516400-184529000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:184520800-184542000	Weak transcription	Ovary	ovary
12	chr1:184521000-184525400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:184521000-184530200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:184521000-184535800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:184521000-184547400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:184523000-184530200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:184524000-184526600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:184524200-184525000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:184524200-184525000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:184524200-184525000	Enhancers	NHEK	skin
21	chr1:184524200-184525400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:184524200-184525400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:184524200-184525600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:184524200-184525800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:184524200-184526000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:184524200-184526400	Enhancers	Right Atrium	heart
27	chr1:184524200-184526600	Enhancers	HMEC	breast
28	chr1:184524200-184528400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr1:184524400-184525000	Enhancers	Brain Cingulate Gyrus	brain
30	chr1:184524400-184525200	Enhancers	Brain Germinal Matrix	brain
31	chr1:184524400-184525400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr1:184524400-184525400	Enhancers	Adipose Nuclei	Adipose
33	chr1:184524400-184525400	Enhancers	Brain Hippocampus Middle	brain
34	chr1:184524400-184525400	Enhancers	Esophagus	oesophagus
35	chr1:184524400-184525600	Enhancers	Fetal Muscle Trunk	muscle
36	chr1:184524400-184525800	Enhancers	Fetal Muscle Leg	muscle
37	chr1:184524400-184526400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:184524400-184526400	Enhancers	Right Ventricle	heart
39	chr1:184524400-184526600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:184524400-184526600	Enhancers	Left Ventricle	heart
41	chr1:184524400-184527200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:184524400-184529200	Enhancers	Psoas Muscle	Psoas
43	chr1:184524600-184525000	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr1:184524600-184525000	Enhancers	Brain Angular Gyrus	brain
45	chr1:184524600-184525000	Enhancers	Fetal Brain Male	brain
46	chr1:184524600-184525200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr1:184524600-184525200	Enhancers	Colon Smooth Muscle	Colon
48	chr1:184524600-184525400	Enhancers	Spleen	Spleen
49	chr1:184524600-184525600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:184524600-184525800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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