Variant report

Variant	rs12022830
Chromosome Location	chr1:62315714-62315715
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	chr1:62313339..62316037-chr1:62320752..62322318,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10157116	0.90[ASN][1000 genomes]
rs12022000	0.87[ASN][1000 genomes]
rs12025222	0.98[ASN][1000 genomes]
rs12029243	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12045057	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17371638	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17380420	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2185136	0.82[AMR][1000 genomes]
rs2275859	1.00[ASN][1000 genomes]
rs57557053	0.98[ASN][1000 genomes]
rs58052322	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58932514	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60422848	0.98[ASN][1000 genomes]
rs7515512	0.98[ASN][1000 genomes]
rs7554677	0.82[AMR][1000 genomes];1.00[ASN][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:53 , 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	chr1:62297800-62321600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:62298000-62330000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:62300200-62321800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:62300800-62321400	Weak transcription	Fetal Intestine Large	intestine
24	chr1:62301400-62320800	Weak transcription	Fetal Intestine Small	intestine
25	chr1:62301400-62331400	Weak transcription	Psoas Muscle	Psoas
26	chr1:62302600-62321400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:62302600-62331400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:62303800-62321600	Weak transcription	Liver	Liver
29	chr1:62305600-62320800	Weak transcription	HMEC	breast
30	chr1:62305600-62321600	Weak transcription	NHEK	skin
31	chr1:62306000-62318200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:62306400-62318000	Weak transcription	HUVEC	blood vessel
33	chr1:62308600-62321600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:62308800-62321000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:62308800-62331600	Weak transcription	Stomach Mucosa	stomach
36	chr1:62309400-62331400	Weak transcription	Gastric	stomach
37	chr1:62310200-62316200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:62311000-62319200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:62311000-62319600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:62311400-62318600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:62311600-62316600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:62311600-62319000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:62311600-62319400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:62311800-62318400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:62312800-62353200	Weak transcription	Colon Smooth Muscle	Colon
46	chr1:62313000-62321600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:62313000-62321800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:62313000-62330200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:62313200-62339400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:62314200-62321200	Weak transcription	Rectal Mucosa Donor 29	rectum

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