Variant report

Variant	rs12080389
Chromosome Location	chr1:173690603-173690604
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173686308..173688392-chr1:173689930..173692042,2	K562	blood:
2	chr1:173684004..173686293-chr1:173689052..173693084,4	MCF-7	breast:
3	chr1:173680351..173683002-chr1:173689911..173692365,2	K562	blood:
4	chr1:173680023..173685703-chr1:173685874..173692365,9	K562	blood:

Variant related genes	Relation type
ENSG00000076321	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10081990	0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10158663	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10399912	0.84[YRI][hapmap]
rs10798298	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10912677	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912678	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912680	0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912682	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912684	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1115487	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11487392	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12065033	1.00[EUR][1000 genomes]
rs12067571	1.00[EUR][1000 genomes]
rs12070556	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12073601	1.00[EUR][1000 genomes]
rs12074150	1.00[EUR][1000 genomes]
rs12082206	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12083423	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12085748	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12085894	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12094130	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12095090	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12096832	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12098124	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1322771	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1322772	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13375555	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1474907	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs16846383	0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs16846395	0.86[YRI][hapmap]
rs16846398	0.86[YRI][hapmap]
rs16846420	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2224657	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs28578576	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs59845733	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6425256	0.86[YRI][hapmap]
rs6425257	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6658217	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6663880	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6670574	1.00[EUR][1000 genomes]
rs6675762	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6686455	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6689764	0.88[AMR][1000 genomes]
rs6691327	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6691922	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6692452	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6695782	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6698348	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6702485	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7518130	0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs7522788	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7534521	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7536773	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7544583	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7550036	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7552840	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9282959	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9282960	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9286886	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9286887	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9286890	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9286894	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425413	0.87[YRI][hapmap]
rs9425414	0.86[YRI][hapmap]
rs9425415	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425418	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425419	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425420	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425421	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425422	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425423	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425424	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425425	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425426	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425734	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425736	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425738	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425740	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425741	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425742	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425746	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425747	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425750	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425751	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425752	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425758	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425759	0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs9425761	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9442660	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9970488	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9970633	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv1014827	chr1:173653453-173692470	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173684800-173695000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:173684800-173702800	Weak transcription	Spleen	Spleen
3	chr1:173685000-173695200	Weak transcription	Esophagus	oesophagus
4	chr1:173685000-173695200	Weak transcription	Pancreas	Pancrea
5	chr1:173685000-173720800	Weak transcription	Small Intestine	intestine
6	chr1:173685200-173692200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:173685200-173692200	Weak transcription	Placenta	Placenta
8	chr1:173685200-173693400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:173685200-173694000	Weak transcription	Left Ventricle	heart
10	chr1:173685200-173694200	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:173685200-173694400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:173685200-173694400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:173685200-173694400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:173685200-173694400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:173685200-173694400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:173685200-173694600	Weak transcription	Colonic Mucosa	Colon
17	chr1:173685200-173724600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:173685400-173691200	Weak transcription	Thymus	Thymus
19	chr1:173685400-173691400	Weak transcription	Aorta	Aorta
20	chr1:173685400-173694000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:173685400-173694200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:173685400-173694400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:173685400-173694400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:173685400-173694400	Weak transcription	Fetal Brain Male	brain
25	chr1:173685400-173702800	Weak transcription	Psoas Muscle	Psoas
26	chr1:173685400-173725000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:173685600-173691200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:173685600-173692200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:173685600-173693800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:173685600-173694200	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:173685600-173694600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:173685600-173702800	Weak transcription	Brain Substantia Nigra	brain
33	chr1:173685800-173690800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:173685800-173692400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:173685800-173693600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:173685800-173702800	Weak transcription	NH-A	brain
37	chr1:173685800-173703000	Weak transcription	Osteobl	bone
38	chr1:173685800-173724800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:173686000-173693800	Weak transcription	HMEC	breast
40	chr1:173686200-173691200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:173686200-173691600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:173686200-173692000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:173686200-173692200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr1:173686200-173694400	Weak transcription	NHLF	lung
45	chr1:173686200-173702800	Weak transcription	NHEK	skin
46	chr1:173686400-173694200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:173686600-173691400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:173686600-173702800	Weak transcription	HSMMtube	muscle
49	chr1:173686800-173691600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr1:173686800-173693800	Weak transcription	Adipose Nuclei	Adipose

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