Variant report

Variant	rs2819853
Chromosome Location	chr6:45412657-45412658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:45412401..45414815-chr6:45415090..45418058,3	K562	blood:
2	chr6:45334941..45336604-chr6:45412002..45413719,2	K562	blood:
3	chr6:45411583..45414532-chr6:45553284..45556066,2	MCF-7	breast:
4	chr6:45409035..45411043-chr6:45411792..45413843,2	MCF-7	breast:
5	chr6:45344606..45346855-chr6:45412406..45414659,2	K562	blood:
6	chr6:45387748..45391708-chr6:45411160..45414695,4	MCF-7	breast:
7	chr6:45403577..45407385-chr6:45411377..45414376,7	K562	blood:
8	chr6:45412131..45416669-chr6:45417302..45422043,11	K562	blood:
9	chr6:45344177..45348784-chr6:45412133..45417901,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000124813	Chromatin interaction
ENSG00000196284	Chromatin interaction
ENSG00000271857	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10214519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12197948	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12210100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12215249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1317777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13208741	1.00[JPT][hapmap]
rs1343799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1934327	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2252718	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2256819	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396442	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2677098	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677099	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677100	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677109	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2677110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790094	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2790095	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2790097	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2790098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790099	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790102	1.00[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs2790103	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2819852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819865	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819866	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2819867	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820339	1.00[CEU][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs2820340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711816	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4714854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6458443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765724	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7756144	0.89[EUR][1000 genomes]
rs910586	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9472494	1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9885645	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2819853	MRPL2	cis	cerebellum	SCAN
rs2819853	RUNX2	cis	multi-tissue	Pritchard

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45394400-45413200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:45399400-45423600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:45402000-45413200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:45403800-45413200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:45405000-45413000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:45405000-45413200	Weak transcription	Brain Anterior Caudate	brain
7	chr6:45405200-45417200	Weak transcription	Spleen	Spleen
8	chr6:45405400-45413400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:45405600-45413200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:45405600-45413200	Weak transcription	Brain Substantia Nigra	brain
11	chr6:45405600-45413400	Weak transcription	Brain Angular Gyrus	brain
12	chr6:45405600-45413800	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:45405600-45417400	Genic enhancers	Dnd41	blood
14	chr6:45407000-45413200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:45407000-45413400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:45407200-45413000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr6:45407200-45413000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:45407200-45413200	Weak transcription	Fetal Kidney	kidney
19	chr6:45407200-45413200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:45407200-45413800	Weak transcription	Aorta	Aorta
21	chr6:45407200-45418200	Weak transcription	Gastric	stomach
22	chr6:45407200-45462000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:45407400-45413000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:45407400-45413600	Weak transcription	Primary T cells from cord blood	blood
25	chr6:45407800-45413200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr6:45407800-45413200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:45409200-45413400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:45409800-45413000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:45410400-45413400	Enhancers	NHDF-Ad	bronchial
30	chr6:45410600-45414000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:45411000-45412800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr6:45411000-45413200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:45411000-45413600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:45411200-45414000	Enhancers	Fetal Thymus	thymus
35	chr6:45411200-45416200	Weak transcription	Lung	lung
36	chr6:45411400-45413000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:45411400-45413000	Weak transcription	HSMMtube	muscle
38	chr6:45411400-45414200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:45411600-45413000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr6:45411600-45413200	Weak transcription	Right Ventricle	heart
41	chr6:45411800-45413200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr6:45411800-45416200	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr6:45412000-45413200	Genic enhancers	Muscle Satellite Cultured Cells	--
44	chr6:45412000-45413200	Genic enhancers	HSMM	muscle
45	chr6:45412000-45413200	Enhancers	K562	blood
46	chr6:45412000-45413400	Enhancers	Duodenum Mucosa	Duodenum
47	chr6:45412000-45413800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:45412000-45413800	Enhancers	NHEK	skin
49	chr6:45412000-45414200	Enhancers	Placenta	Placenta
50	chr6:45412000-45415600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links