Variant report

Variant	rs7928810
Chromosome Location	chr11:17372443-17372444
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:17372413-17375723	NB4	blood:	n/a	n/a
2	MXI1	chr11:17372217-17373803	IMR90	lung:	n/a	n/a
3	RCOR1	chr11:17372301-17372652	K562	blood:	n/a	n/a
4	MAFK	chr11:17372419-17372617	HepG2	liver:	n/a	chr11:17372481-17372496 chr11:17372485-17372499
5	CTCF	chr11:17372360-17372510	GM12873	blood:	n/a	n/a
6	MYC	chr11:17372411-17373764	NB4	blood:	n/a	n/a
7	CTCF	chr11:17372440-17372590	AG09319	gingival:	n/a	n/a
8	POLR2A	chr11:17371970-17373803	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:17368260..17372452-chr11:17372695..17374422,3	K562	blood:
2	chr11:17324227..17326282-chr11:17370624..17372568,2	K562	blood:
3	chr11:17294885..17299963-chr11:17371989..17377835,11	K562	blood:

Variant related genes	Relation type
NCR3LG1	TF binding region
ENSG00000070081	Chromatin interaction
ENSG00000188211	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1002226	0.88[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs10832776	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10832778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11024268	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11024271	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12146443	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12146652	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1557765	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs2051772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2074314	1.00[ASW][hapmap];0.85[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap]
rs214091	1.00[LWK][hapmap]
rs214105	1.00[LWK][hapmap]
rs4439492	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5215	0.88[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs7124355	0.85[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap]
rs7484027	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs757081	1.00[LWK][hapmap]
rs757110	0.88[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7928810	SAA4	cis	parietal	SCAN
rs7928810	RP1-239B22.5	cis	Esophagus Mucosa	GTEx
rs7928810	NCR3LG1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17308200-17372600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr11:17336200-17372600	Weak transcription	HUVEC	blood vessel
3	chr11:17354400-17373000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:17356000-17372600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:17356000-17372600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr11:17356000-17372800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr11:17356000-17372800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:17356200-17372600	Weak transcription	Adipose Nuclei	Adipose
9	chr11:17356200-17372800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr11:17356200-17372800	Weak transcription	Aorta	Aorta
11	chr11:17356200-17372800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr11:17356200-17372800	Weak transcription	Ovary	ovary
13	chr11:17356200-17373000	Weak transcription	Left Ventricle	heart
14	chr11:17356400-17373000	Weak transcription	Esophagus	oesophagus
15	chr11:17365400-17372600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr11:17365600-17372600	Weak transcription	Osteobl	bone
17	chr11:17365800-17372800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:17365800-17372800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr11:17365800-17372800	Weak transcription	NH-A	brain
20	chr11:17366000-17372600	Weak transcription	NHLF	lung
21	chr11:17366000-17372800	Weak transcription	HMEC	breast
22	chr11:17366200-17373000	Weak transcription	NHEK	skin
23	chr11:17366600-17372600	Weak transcription	Primary T cells from cord blood	blood
24	chr11:17368400-17372800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr11:17369600-17373200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:17369800-17372800	Weak transcription	HSMMtube	muscle
27	chr11:17371200-17372600	Weak transcription	Fetal Thymus	thymus
28	chr11:17371400-17372600	Weak transcription	Thymus	Thymus
29	chr11:17371600-17372600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr11:17372000-17372800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:17372200-17372600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:17372200-17373000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:17372400-17372600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr11:17372400-17372600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr11:17372400-17372600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:17372400-17372600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:17372400-17372800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
38	chr11:17372400-17372800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr11:17372400-17372800	Enhancers	Brain Angular Gyrus	brain
40	chr11:17372400-17372800	Enhancers	Duodenum Mucosa	Duodenum
41	chr11:17372400-17372800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
42	chr11:17372400-17373000	Active TSS	Liver	Liver
43	chr11:17372400-17373000	Enhancers	Colonic Mucosa	Colon
44	chr11:17372400-17373000	Enhancers	A549	lung
45	chr11:17372400-17373000	Enhancers	Dnd41	blood
46	chr11:17372400-17373000	Bivalent/Poised TSS	GM12878-XiMat	blood
47	chr11:17372400-17373400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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