Variant report

Variant	rs11880894
Chromosome Location	chr19:38981539-38981540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38978849..38981748-chr19:38997684..38999200,2	K562	blood:
2	chr19:38979413..38981714-chr19:38996076..38997616,2	K562	blood:
3	chr19:38981492..38983991-chr19:38986768..38989553,3	K562	blood:
4	chr19:38980741..38983554-chr19:39086276..39088522,2	K562	blood:
5	chr19:38979413..38982321-chr19:38995357..38997616,3	K562	blood:

Variant related genes	Relation type
ENSG00000267291	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000196218	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11880533	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880546	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882813	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882920	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972651	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.99[MKK][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs16972654	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs34370689	0.88[EUR][1000 genomes]
rs35968585	0.81[ASN][1000 genomes]
rs55845760	0.85[ASN][1000 genomes]
rs55854019	0.93[ASN][1000 genomes]
rs56081639	0.85[ASN][1000 genomes]
rs56082081	0.82[ASN][1000 genomes]
rs56271299	0.89[ASN][1000 genomes]
rs56278664	0.85[ASN][1000 genomes]
rs56356303	0.89[ASN][1000 genomes]
rs57127300	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs57257936	0.93[ASN][1000 genomes]
rs58636221	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59200109	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6508804	0.93[ASN][1000 genomes]
rs71356808	0.81[ASN][1000 genomes]
rs7245897	0.85[ASN][1000 genomes]
rs7246023	0.85[ASN][1000 genomes]
rs7246905	0.85[ASN][1000 genomes]
rs7252028	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252837	0.85[ASN][1000 genomes]
rs7253112	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259884	0.85[ASN][1000 genomes]
rs73541002	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
3	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv833824	chr19:38914618-39084758	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	esv1816081	chr19:38919971-39050479	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv911664	chr19:38924814-39048163	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv911665	chr19:38924814-39101879	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv911666	chr19:38948356-39014184	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11880894	ZNF780B	cis	parietal	SCAN
rs11880894	LGALS13	cis	cerebellum	SCAN
rs11880894	ZNF223	cis	cerebellum	SCAN
rs11880894	SPTBN4	cis	cerebellum	SCAN
rs11880894	PHLDB3	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38929800-38984400	Weak transcription	Psoas Muscle	Psoas
2	chr19:38934800-39005600	Strong transcription	Fetal Muscle Leg	muscle
3	chr19:38938600-38987600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:38940000-39006400	Weak transcription	HSMM	muscle
5	chr19:38947600-38997400	Strong transcription	Fetal Muscle Trunk	muscle
6	chr19:38960400-38994600	Weak transcription	Brain Angular Gyrus	brain
7	chr19:38960800-39034400	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr19:38963000-39033000	Strong transcription	Skeletal Muscle Male	skeletal muscle
9	chr19:38972200-38984000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr19:38973200-38981800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
11	chr19:38973600-38982000	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr19:38973600-38984200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr19:38974200-38984600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:38975800-38985000	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr19:38975800-38996600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr19:38976200-38984200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:38976800-38986800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:38976800-39005400	Weak transcription	Brain Anterior Caudate	brain
19	chr19:38977200-38996600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:38979000-38985000	Weak transcription	Gastric	stomach
21	chr19:38980600-38984400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:38980800-38981600	Strong transcription	Brain Substantia Nigra	brain
23	chr19:38981000-38981800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
24	chr19:38981000-38984600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:38981200-38981600	ZNF genes & repeats	Adipose Nuclei	Adipose
26	chr19:38981200-38981800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
27	chr19:38981400-38982200	ZNF genes & repeats	Brain Hippocampus Middle	brain
28	chr19:38981400-38992400	Strong transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links