Variant report

Variant	rs72797519
Chromosome Location	chr2:55362756-55362757
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55272140..55279868-chr2:55356344..55371606,28	K562	blood:
2	chr2:55269242..55271326-chr2:55360631..55363213,2	K562	blood:
3	chr2:55275855..55279437-chr2:55359990..55364186,7	K562	blood:
4	chr2:55350017..55352674-chr2:55360663..55363208,2	K562	blood:
5	chr2:55354045..55358992-chr2:55359264..55362961,10	K562	blood:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10194457	0.89[ASN][1000 genomes]
rs11892071	0.87[EUR][1000 genomes]
rs4233958	0.89[ASN][1000 genomes]
rs4672022	0.89[ASN][1000 genomes]
rs55691469	0.96[EUR][1000 genomes]
rs55875262	0.91[EUR][1000 genomes]
rs56056614	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56073856	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56231606	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56285641	0.89[EUR][1000 genomes]
rs58680169	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6721769	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6721928	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6731596	0.89[ASN][1000 genomes]
rs6745066	0.90[ASN][1000 genomes]
rs72795491	0.91[EUR][1000 genomes]
rs72795493	0.91[EUR][1000 genomes]
rs72795498	0.91[EUR][1000 genomes]
rs72795499	0.84[EUR][1000 genomes]
rs72797513	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797515	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797516	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797517	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797522	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797530	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72797534	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72797535	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72797536	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72797537	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7575639	0.89[ASN][1000 genomes]
rs7585618	0.89[ASN][1000 genomes]
rs9789426	0.91[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72797519	CLHC1	cis	Artery Tibial	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55361000-55363000	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr2:55361000-55364000	Weak transcription	Left Ventricle	heart
3	chr2:55361200-55364400	Weak transcription	Right Ventricle	heart
4	chr2:55361200-55365400	Enhancers	Fetal Intestine Small	intestine
5	chr2:55361400-55366400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr2:55361400-55370200	Enhancers	Fetal Intestine Large	intestine
7	chr2:55361600-55363200	Enhancers	Brain Cingulate Gyrus	brain
8	chr2:55361600-55363400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:55361600-55363400	Enhancers	Duodenum Mucosa	Duodenum
10	chr2:55361600-55363400	Weak transcription	Right Atrium	heart
11	chr2:55361600-55364000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:55361600-55364000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:55361600-55364200	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr2:55361600-55364200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:55361600-55364400	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr2:55361600-55365200	Enhancers	K562	blood
17	chr2:55361600-55365400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:55361600-55366000	Enhancers	Primary hematopoietic stem cells	blood
19	chr2:55361600-55368200	Weak transcription	Esophagus	oesophagus
20	chr2:55361800-55362800	Enhancers	Primary B cells from peripheral blood	blood
21	chr2:55361800-55363000	Weak transcription	Fetal Brain Male	brain
22	chr2:55361800-55363200	Enhancers	Brain Hippocampus Middle	brain
23	chr2:55361800-55363200	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr2:55361800-55363200	Enhancers	Stomach Mucosa	stomach
25	chr2:55361800-55363400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:55361800-55363400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:55361800-55363600	Enhancers	Primary T cells fromperipheralblood	blood
28	chr2:55361800-55363600	Enhancers	Brain Substantia Nigra	brain
29	chr2:55361800-55363800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:55361800-55364000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:55361800-55364000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr2:55361800-55364400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:55361800-55365000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:55361800-55365200	Enhancers	Brain Germinal Matrix	brain
35	chr2:55361800-55365200	Weak transcription	Fetal Heart	heart
36	chr2:55361800-55366800	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr2:55361800-55366800	Weak transcription	Hela-S3	cervix
38	chr2:55361800-55367800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr2:55361800-55368000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:55361800-55368600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:55361800-55368800	Weak transcription	A549	lung
42	chr2:55361800-55373000	Weak transcription	HSMMtube	muscle
43	chr2:55361800-55378600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:55362000-55363000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:55362000-55363200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:55362000-55363200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr2:55362000-55363400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:55362000-55363400	Weak transcription	GM12878-XiMat	blood
49	chr2:55362000-55363600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:55362000-55363600	Weak transcription	Fetal Stomach	stomach

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