Variant report

Variant	rs12135923
Chromosome Location	chr1:62406650-62406651
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10889271	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10889272	0.83[ASN][1000 genomes]
rs10889277	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10889278	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10889279	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11207869	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11207877	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11207878	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2498954	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35506226	0.86[EUR][1000 genomes]
rs3737108	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61775620	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6668270	0.85[ASN][1000 genomes]
rs6698695	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7512525	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530734	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[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	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
2	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
3	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
4	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1110	chr1:62395723-62454435	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv546415	chr1:62405873-62437872	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 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	chr1:62336000-62408600	Weak transcription	Pancreas	Pancrea
2	chr1:62346200-62417600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:62350600-62428200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:62350800-62417600	Weak transcription	Ovary	ovary
5	chr1:62353800-62408800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:62361600-62408800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:62362000-62408600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:62372400-62408800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:62372400-62417600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:62374600-62410600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:62376200-62417600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:62380600-62408600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:62380800-62410000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:62381000-62408200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:62381000-62416000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:62381200-62417400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:62381200-62418400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:62383400-62408000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:62384600-62408200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:62384600-62408800	Weak transcription	Fetal Intestine Large	intestine
21	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
22	chr1:62385400-62408400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:62385400-62408600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:62386000-62408600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:62391800-62409000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:62392000-62408800	Weak transcription	Gastric	stomach
27	chr1:62392600-62408600	Weak transcription	Stomach Mucosa	stomach
28	chr1:62392600-62408800	Weak transcription	Left Ventricle	heart
29	chr1:62393800-62422400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:62395000-62408600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:62395000-62410800	Weak transcription	Liver	Liver
32	chr1:62395800-62408200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:62396200-62408600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:62396200-62416000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:62396200-62417200	Weak transcription	HMEC	breast
36	chr1:62396400-62408200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:62396400-62408600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:62396400-62418000	Weak transcription	Fetal Kidney	kidney
39	chr1:62397400-62408200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:62397600-62408600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:62398000-62408200	Weak transcription	NHEK	skin
42	chr1:62398200-62408400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:62398200-62408600	Weak transcription	Esophagus	oesophagus
44	chr1:62398800-62408600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:62400600-62417600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:62401400-62408800	Weak transcription	Lung	lung
47	chr1:62403000-62407600	Weak transcription	HepG2	liver
48	chr1:62404200-62407000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:62405600-62407200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:62406000-62408000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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