Variant report

Variant	rs56864802
Chromosome Location	chr1:174568929-174568930
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174566765..174568988-chr1:174739021..174740535,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10489261	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16847018	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16847025	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16847121	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16847206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2179108	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2179109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2901819	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41266052	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41397546	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4515855	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57132183	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57243929	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57648142	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57898822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58063264	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58525721	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs58762254	0.83[EUR][1000 genomes]
rs59190079	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59262554	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59354288	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59436654	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60240702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60665754	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60723087	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60865584	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60885521	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61028529	0.83[EUR][1000 genomes]
rs61329817	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6673649	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6692753	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6695956	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6703536	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7543502	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7547843	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1014753	chr1:174271770-174694838	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv999295	chr1:174457532-174596961	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv534381	chr1:174468168-174656796	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv2757762	chr1:174469281-174569776	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv2758979	chr1:174469281-174569776	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv3434296	chr1:174556344-174594264	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56864802	CRYM	trans	lymphoblastoid	RTeQTL
rs56864802	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174546000-174573000	Weak transcription	Left Ventricle	heart
2	chr1:174553600-174570200	Weak transcription	Gastric	stomach
3	chr1:174555000-174574000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:174555000-174575000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:174566400-174570200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:174566800-174569800	Weak transcription	Primary T cells from cord blood	blood
7	chr1:174566800-174586600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:174568200-174572800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:174568400-174572400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:174568400-174572400	Weak transcription	Thymus	Thymus
11	chr1:174568400-174588800	Weak transcription	Esophagus	oesophagus
12	chr1:174568600-174574200	Weak transcription	Rectal Mucosa Donor 31	rectum

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