Variant report

Variant	rs12408105
Chromosome Location	chr1:62311980-62311981
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	chr1:62304428..62307569-chr1:62310144..62313240,3	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12402847	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12408315	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12410306	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12728331	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12749061	0.92[MEX][hapmap];0.81[AMR][1000 genomes]
rs1286815	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2938	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34403905	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34473594	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35180388	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35318456	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35722784	0.83[AMR][1000 genomes]
rs71641748	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3693319	chr1:62207254-62402549	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv830004	chr1:62242944-62382228	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv1099	chr1:62275317-62315943	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 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	chr1:62228600-62391800	Weak transcription	Small Intestine	intestine
2	chr1:62263800-62343600	Weak transcription	Colonic Mucosa	Colon
3	chr1:62264600-62321600	Weak transcription	Pancreas	Pancrea
4	chr1:62264600-62335600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:62271800-62329800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:62278200-62316400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:62285600-62338000	Weak transcription	Fetal Kidney	kidney
8	chr1:62290800-62326000	Weak transcription	Left Ventricle	heart
9	chr1:62293800-62321600	Weak transcription	Esophagus	oesophagus
10	chr1:62293800-62343200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:62294400-62330200	Weak transcription	Fetal Stomach	stomach
12	chr1:62294600-62321000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:62294800-62324000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:62295000-62322600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:62295800-62321600	Weak transcription	Primary T cells from cord blood	blood
16	chr1:62296000-62321400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:62296000-62321400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:62296200-62321600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:62297400-62321400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:62297800-62313800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr1:62297800-62321600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:62298000-62330000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:62300200-62321800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:62300800-62321400	Weak transcription	Fetal Intestine Large	intestine
25	chr1:62301400-62320800	Weak transcription	Fetal Intestine Small	intestine
26	chr1:62301400-62331400	Weak transcription	Psoas Muscle	Psoas
27	chr1:62302600-62321400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:62302600-62331400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:62303800-62321600	Weak transcription	Liver	Liver
30	chr1:62305600-62320800	Weak transcription	HMEC	breast
31	chr1:62305600-62321600	Weak transcription	NHEK	skin
32	chr1:62305800-62312400	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:62306000-62312000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:62306000-62312200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:62306000-62318200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:62306400-62318000	Weak transcription	HUVEC	blood vessel
37	chr1:62308000-62314000	Weak transcription	Aorta	Aorta
38	chr1:62308600-62321600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:62308800-62321000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:62308800-62331600	Weak transcription	Stomach Mucosa	stomach
41	chr1:62309400-62331400	Weak transcription	Gastric	stomach
42	chr1:62310200-62316200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:62310600-62312200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:62311000-62319200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:62311000-62319600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:62311400-62313000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:62311400-62318600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:62311600-62312000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:62311600-62316600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:62311600-62319000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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