Variant report

Variant	rs12080238
Chromosome Location	chr1:165709018-165709019
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:165706758..165709528-chr1:165795041..165797748,2	K562	blood:
2	chr1:165706527..165709432-chr1:165711887..165713533,2	K562	blood:
3	chr1:165701078..165702896-chr1:165706943..165709704,2	K562	blood:
4	chr1:165707082..165709432-chr1:165711887..165713591,2	K562	blood:

Variant related genes	Relation type
ENSG00000143183	Chromatin interaction
ENSG00000143179	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10800161	1.00[AFR][1000 genomes]
rs10918267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918280	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10918282	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10918286	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10918288	1.00[AFR][1000 genomes]
rs12060158	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12061566	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12062594	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12064088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12064187	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12064466	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12072636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12074976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12075644	1.00[CHB][hapmap]
rs12076579	1.00[EUR][1000 genomes]
rs12077778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12077875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12079073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12082722	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12090132	1.00[EUR][1000 genomes]
rs12094467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12354157	1.00[EUR][1000 genomes]
rs12401468	0.83[AMR][1000 genomes]
rs12566281	1.00[AFR][1000 genomes]
rs28735603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9970857	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	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165685200-165721600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:165687600-165709800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:165687600-165709800	Weak transcription	HUVEC	blood vessel
4	chr1:165687600-165737600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:165687800-165709800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:165690200-165710800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:165691000-165710000	Weak transcription	Fetal Kidney	kidney
8	chr1:165693400-165709600	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:165694000-165709800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:165694000-165709800	Weak transcription	Brain Substantia Nigra	brain
11	chr1:165694000-165711800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:165694200-165709800	Weak transcription	Colonic Mucosa	Colon
13	chr1:165694200-165709800	Weak transcription	Pancreas	Pancrea
14	chr1:165694200-165709800	Weak transcription	Spleen	Spleen
15	chr1:165694200-165710000	Weak transcription	NHEK	skin
16	chr1:165694200-165721600	Weak transcription	Aorta	Aorta
17	chr1:165694200-165721600	Weak transcription	Esophagus	oesophagus
18	chr1:165694400-165721600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:165694600-165709800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:165694600-165711000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:165694600-165711000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:165694600-165736800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr1:165694800-165709800	Weak transcription	Small Intestine	intestine
24	chr1:165695600-165709800	Weak transcription	Brain Angular Gyrus	brain
25	chr1:165695800-165712000	Weak transcription	Psoas Muscle	Psoas
26	chr1:165696000-165709800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:165696000-165721600	Weak transcription	Gastric	stomach
28	chr1:165696400-165709200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:165696800-165709800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:165696800-165709800	Weak transcription	Brain Germinal Matrix	brain
31	chr1:165696800-165709800	Weak transcription	NHLF	lung
32	chr1:165697200-165709800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:165697200-165710400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:165697400-165709600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:165697400-165709800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:165697400-165709800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:165697400-165709800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:165697400-165709800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:165697400-165709800	Weak transcription	HMEC	breast
40	chr1:165697400-165709800	Weak transcription	HSMMtube	muscle
41	chr1:165697400-165710000	Weak transcription	NHDF-Ad	bronchial
42	chr1:165697600-165709800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr1:165698000-165709800	Weak transcription	Brain Anterior Caudate	brain
44	chr1:165698000-165709800	Weak transcription	Placenta	Placenta
45	chr1:165698200-165709800	Weak transcription	Stomach Mucosa	stomach
46	chr1:165698600-165709400	Weak transcription	Right Ventricle	heart
47	chr1:165699800-165721600	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr1:165700400-165709200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:165702800-165714600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:165703200-165709800	Weak transcription	Rectal Mucosa Donor 31	rectum

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