Variant report

Variant	rs56285641
Chromosome Location	chr2:55350682-55350683
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55273963..55277742-chr2:55344682..55351127,9	K562	blood:
2	chr2:55348151..55351160-chr2:55366268..55368623,3	K562	blood:
3	chr2:55350017..55352674-chr2:55360663..55363208,2	K562	blood:
4	chr2:55287127..55289595-chr2:55348601..55351225,2	K562	blood:
5	chr2:55347566..55351333-chr2:55355556..55357913,4	K562	blood:
6	chr2:55274620..55276240-chr2:55348004..55351084,3	K562	blood:
7	chr2:55319141..55322072-chr2:55348443..55351423,2	K562	blood:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11892071	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920844	0.81[ASN][1000 genomes]
rs2968781	0.81[ASN][1000 genomes]
rs55691469	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55875262	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56056614	0.91[EUR][1000 genomes]
rs56073856	0.91[EUR][1000 genomes]
rs56231606	0.91[EUR][1000 genomes]
rs58680169	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6721769	0.91[EUR][1000 genomes]
rs6721928	0.91[EUR][1000 genomes]
rs72795491	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795493	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72795498	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795499	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797513	0.91[EUR][1000 genomes]
rs72797515	0.91[EUR][1000 genomes]
rs72797516	0.91[EUR][1000 genomes]
rs72797517	0.91[EUR][1000 genomes]
rs72797519	0.89[EUR][1000 genomes]
rs72797522	0.91[EUR][1000 genomes]
rs72797530	0.91[EUR][1000 genomes]
rs72797534	0.91[EUR][1000 genomes]
rs72797535	0.91[EUR][1000 genomes]
rs72797536	0.91[EUR][1000 genomes]
rs72797537	0.91[EUR][1000 genomes]
rs9789426	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56285641	CLHC1	cis	Artery Tibial	GTEx
rs56285641	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55337200-55351000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:55339400-55351000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:55346000-55351600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr2:55346600-55350800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:55347400-55351000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:55347400-55351000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:55347400-55351000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:55347600-55360600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:55347800-55351000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:55348000-55351000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:55348000-55351000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:55348200-55351200	Weak transcription	Fetal Intestine Small	intestine
13	chr2:55348200-55360600	Weak transcription	Stomach Mucosa	stomach
14	chr2:55348400-55351000	Weak transcription	Fetal Intestine Large	intestine
15	chr2:55348400-55360400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:55348600-55350800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:55348600-55351000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:55348600-55360800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:55348800-55351000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:55348800-55351000	Weak transcription	HSMMtube	muscle
21	chr2:55348800-55360400	Weak transcription	NHDF-Ad	bronchial
22	chr2:55349600-55351000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:55349600-55351600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:55349800-55360600	Weak transcription	Fetal Stomach	stomach
25	chr2:55350000-55351000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:55350000-55351000	Weak transcription	Aorta	Aorta
27	chr2:55350000-55351200	Weak transcription	Left Ventricle	heart
28	chr2:55350000-55352400	Weak transcription	Pancreas	Pancrea
29	chr2:55350000-55355200	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:55350000-55360600	Weak transcription	Psoas Muscle	Psoas
31	chr2:55350000-55360800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:55350000-55360800	Weak transcription	Lung	lung
33	chr2:55350000-55360800	Weak transcription	Ovary	ovary
34	chr2:55350200-55351000	Weak transcription	Brain Germinal Matrix	brain
35	chr2:55350200-55351000	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:55350200-55351200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:55350200-55351200	Weak transcription	Brain Angular Gyrus	brain
38	chr2:55350200-55351200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:55350200-55351200	Weak transcription	Brain Substantia Nigra	brain
40	chr2:55350200-55354400	Weak transcription	K562	blood
41	chr2:55350200-55355200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:55350200-55356400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr2:55350400-55350800	Weak transcription	Brain Anterior Caudate	brain
44	chr2:55350600-55351000	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links