Variant report

Variant	rs12130397
Chromosome Location	chr1:179964009-179964010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10442618	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10494524	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12118985	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12120418	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12121834	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12121845	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12123139	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12123201	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12123560	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12124265	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12125556	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12125693	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12125893	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12130479	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12130489	0.83[EUR][1000 genomes]
rs12130675	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12132694	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12134536	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12135751	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12135828	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12138201	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12138974	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12139040	0.84[EUR][1000 genomes]
rs12139323	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12139412	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12139761	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12140235	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12140589	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140622	0.84[EUR][1000 genomes]
rs12140868	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12141817	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12144275	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12144853	0.82[EUR][1000 genomes]
rs12145411	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12184270	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16843139	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16855014	0.84[ASN][1000 genomes]
rs16855019	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855021	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855022	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855025	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855048	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855049	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855052	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855070	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855107	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16855110	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16855125	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16855130	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16855268	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16855270	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17371159	0.84[EUR][1000 genomes]
rs3856048	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4266842	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4278337	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4460595	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57165548	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58316647	0.84[ASN][1000 genomes]
rs58463801	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58749862	0.84[ASN][1000 genomes]
rs59132689	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60972670	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61014689	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61242295	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73032352	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73032390	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73032397	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73034408	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73034486	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73039990	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73039999	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73040001	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9699897	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv466228	chr1:179944901-180067988	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv548340	chr1:179944901-180067988	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv520322	chr1:179944901-180071987	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv548341	chr1:179945390-180067914	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv548342	chr1:179958809-180067988	Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv548343	chr1:179958809-180071987	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv548344	chr1:179960787-180071987	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179927000-179965600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:179938000-179983200	Weak transcription	Brain Germinal Matrix	brain
3	chr1:179938600-179965800	Weak transcription	Esophagus	oesophagus
4	chr1:179938600-179975800	Weak transcription	Thymus	Thymus
5	chr1:179938600-179983200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:179938600-179984600	Weak transcription	Lung	lung
7	chr1:179939000-179989000	Weak transcription	Gastric	stomach
8	chr1:179939800-179974800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:179941400-180031800	Weak transcription	Spleen	Spleen
10	chr1:179946400-179965600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:179946400-179972800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:179946400-179983000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:179946400-179989200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:179946600-179965800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:179946600-179965800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:179946600-179983200	Weak transcription	Brain Angular Gyrus	brain
17	chr1:179947800-179989400	Weak transcription	Small Intestine	intestine
18	chr1:179948400-179965800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:179948400-179971800	Weak transcription	Fetal Heart	heart
20	chr1:179948600-179983200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:179949400-179980600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:179950000-179980600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:179950200-179966000	Weak transcription	Fetal Brain Female	brain
24	chr1:179951400-179972200	Weak transcription	Psoas Muscle	Psoas
25	chr1:179951400-179974600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:179951800-179974800	Weak transcription	Hela-S3	cervix
27	chr1:179952400-179965600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:179953400-179965400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:179953600-179964800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr1:179953600-179965800	Weak transcription	Brain Substantia Nigra	brain
31	chr1:179953600-179971400	Weak transcription	HMEC	breast
32	chr1:179953800-179965800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:179954200-179965800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:179954200-179975400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:179954600-179967000	Strong transcription	Fetal Thymus	thymus
36	chr1:179954600-179975600	Weak transcription	Fetal Kidney	kidney
37	chr1:179954800-179971200	Weak transcription	NHEK	skin
38	chr1:179955000-179989200	Weak transcription	Aorta	Aorta
39	chr1:179955600-179967400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:179955800-179965800	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:179955800-179966600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:179955800-179983000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:179956400-179970000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:179956800-179967000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr1:179956800-179989400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:179957000-179975800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:179957400-179965600	Weak transcription	Ovary	ovary
48	chr1:179957400-179965800	Weak transcription	Pancreas	Pancrea
49	chr1:179957800-179964200	Weak transcription	Fetal Lung	lung
50	chr1:179957800-179965800	Weak transcription	Primary B cells from cord blood	blood

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