Variant report

Variant	rs72797530
Chromosome Location	chr2:55364079-55364080
allele	C/T
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	chr2:55362876..55365443-chr2:55367028..55369648,3	MCF-7	breast:
3	chr2:55275855..55279437-chr2:55359990..55364186,7	K562	blood:
4	chr2:55363727..55366585-chr7:158919602..158922581,2	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	0.90[ASN][1000 genomes]
rs11892071	0.89[EUR][1000 genomes]
rs4233958	0.90[ASN][1000 genomes]
rs4672022	0.90[ASN][1000 genomes]
rs55691469	0.98[EUR][1000 genomes]
rs55875262	0.92[EUR][1000 genomes]
rs56056614	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56073856	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56231606	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56285641	0.91[EUR][1000 genomes]
rs58680169	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6721769	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721928	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731596	0.90[ASN][1000 genomes]
rs6745066	0.91[ASN][1000 genomes]
rs72795491	0.92[EUR][1000 genomes]
rs72795493	0.92[EUR][1000 genomes]
rs72795498	0.92[EUR][1000 genomes]
rs72795499	0.86[EUR][1000 genomes]
rs72797513	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72797515	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72797516	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72797517	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72797519	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72797522	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72797534	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797535	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797536	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797537	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575639	0.90[ASN][1000 genomes]
rs7585618	0.90[ASN][1000 genomes]
rs9789426	0.92[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72797530	CLHC1	cis	Artery Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55361200-55364400	Weak transcription	Right Ventricle	heart
2	chr2:55361200-55365400	Enhancers	Fetal Intestine Small	intestine
3	chr2:55361400-55366400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr2:55361400-55370200	Enhancers	Fetal Intestine Large	intestine
5	chr2:55361600-55364200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr2:55361600-55364200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:55361600-55364400	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr2:55361600-55365200	Enhancers	K562	blood
9	chr2:55361600-55365400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:55361600-55366000	Enhancers	Primary hematopoietic stem cells	blood
11	chr2:55361600-55368200	Weak transcription	Esophagus	oesophagus
12	chr2:55361800-55364400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:55361800-55365000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:55361800-55365200	Enhancers	Brain Germinal Matrix	brain
15	chr2:55361800-55365200	Weak transcription	Fetal Heart	heart
16	chr2:55361800-55366800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr2:55361800-55366800	Weak transcription	Hela-S3	cervix
18	chr2:55361800-55367800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:55361800-55368000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:55361800-55368600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:55361800-55368800	Weak transcription	A549	lung
22	chr2:55361800-55373000	Weak transcription	HSMMtube	muscle
23	chr2:55361800-55378600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:55362000-55364200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr2:55362000-55365200	Weak transcription	Fetal Brain Female	brain
26	chr2:55362000-55366600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:55362000-55366600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:55362200-55364200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:55362200-55364400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:55362200-55364400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:55362200-55364600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr2:55362200-55364600	Weak transcription	Ovary	ovary
33	chr2:55362200-55365200	Weak transcription	Fetal Kidney	kidney
34	chr2:55362200-55367600	Weak transcription	Dnd41	blood
35	chr2:55362200-55369000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:55362400-55368800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:55362800-55364200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr2:55362800-55364800	Enhancers	Fetal Thymus	thymus
39	chr2:55362800-55366000	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr2:55362800-55366600	Enhancers	Placenta	Placenta
41	chr2:55363000-55366000	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr2:55363000-55366200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:55363000-55366400	Enhancers	Fetal Brain Male	brain
44	chr2:55363200-55365000	Enhancers	Primary B cells from peripheral blood	blood
45	chr2:55363200-55365600	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr2:55363200-55366000	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr2:55363200-55366000	Enhancers	H1 Cell Line	embryonic stem cell
48	chr2:55363200-55366200	Enhancers	Colon Smooth Muscle	Colon
49	chr2:55363200-55366800	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr2:55363200-55367200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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