Variant report

Variant	rs2038308
Chromosome Location	chr1:184512912-184512913
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	chr1:184501312..184504109-chr1:184512326..184514186,2	MCF-7	breast:
2	chr1:184509375..184512028-chr1:184512395..184515613,3	MCF-7	breast:

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

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

rs_ID	r²[population]
rs1007224	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797971	0.81[AFR][1000 genomes]
rs10797972	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.83[MEX][hapmap]
rs10797974	0.83[EUR][1000 genomes]
rs10797977	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911606	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12125349	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12127674	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1339563	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1339564	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1339565	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1339566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1339567	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1416752	0.92[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs1569842	0.87[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap]
rs1884200	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1969684	0.83[ASN][1000 genomes]
rs2001270	0.88[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs2038307	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2144294	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2180073	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]
rs2180077	0.87[CHB][hapmap]
rs2890014	0.85[EUR][1000 genomes]
rs2890015	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4650667	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4651208	0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[MKK][hapmap]
rs4651210	0.92[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs4651211	0.93[EUR][1000 genomes]
rs4651213	0.89[CEU][hapmap];0.81[TSI][hapmap]
rs4651217	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4651218	0.85[EUR][1000 genomes]
rs4651219	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666704	0.89[EUR][1000 genomes]
rs7517518	0.89[EUR][1000 genomes]
rs7533466	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7544240	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9970984	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9970990	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[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	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:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184502400-184517000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:184502400-184520200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:184502600-184527200	Weak transcription	Fetal Brain Female	brain
4	chr1:184503200-184514600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:184503200-184516400	Weak transcription	Fetal Brain Male	brain
6	chr1:184503400-184515800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:184503400-184520400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:184504200-184522600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:184505800-184513000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:184505800-184514600	Weak transcription	NHLF	lung
11	chr1:184505800-184515000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:184505800-184515800	Weak transcription	Lung	lung
13	chr1:184505800-184516000	Weak transcription	Pancreas	Pancrea
14	chr1:184505800-184518200	Weak transcription	Gastric	stomach
15	chr1:184505800-184524000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:184505800-184530800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:184505800-184531600	Weak transcription	Fetal Stomach	stomach
18	chr1:184506200-184520600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:184508000-184516600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:184508400-184514000	Weak transcription	Esophagus	oesophagus
21	chr1:184508400-184515000	Weak transcription	NHDF-Ad	bronchial
22	chr1:184508600-184514200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:184509800-184513800	Weak transcription	Psoas Muscle	Psoas
24	chr1:184511000-184514600	Weak transcription	Right Atrium	heart
25	chr1:184511200-184514000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:184511200-184515000	Weak transcription	Placenta	Placenta
27	chr1:184511400-184517200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:184511400-184530400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:184511600-184514800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:184511600-184515800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:184511800-184513600	Weak transcription	HMEC	breast
32	chr1:184511800-184516000	Weak transcription	Right Ventricle	heart
33	chr1:184511800-184524600	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:184512000-184513000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:184512000-184516000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:184512000-184520200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:184512200-184513600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:184512200-184514000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:184512200-184514600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:184512200-184514600	Enhancers	NHEK	skin
41	chr1:184512200-184515000	Weak transcription	Fetal Kidney	kidney
42	chr1:184512200-184516000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr1:184512200-184516000	Weak transcription	Left Ventricle	heart
44	chr1:184512200-184524200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:184512200-184524400	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:184512200-184530200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:184512200-184543600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:184512400-184513800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:184512400-184530200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:184512600-184516200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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