Variant report

Variant	rs4859879
Chromosome Location	chr4:78722315-78722316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78717746..78719654-chr4:78721181..78723626,2	K562	blood:
2	chr4:78714074..78716537-chr4:78722174..78724002,2	K562	blood:
3	chr4:78721732..78724295-chr4:78733166..78737485,4	K562	blood:
4	chr4:78718708..78721606-chr4:78722272..78724950,3	K562	blood:
5	chr4:78720260..78722525-chr4:78782700..78784492,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169288	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10033527	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10033613	0.94[ASN][1000 genomes]
rs11097938	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[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11728886	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11729215	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12645742	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13101418	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs13101987	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13103035	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13103523	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13104947	0.82[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs13106067	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13119606	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13120272	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16996915	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2134050	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28404443	0.88[ASN][1000 genomes]
rs28855210	0.83[ASN][1000 genomes]
rs34830788	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35735677	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4453957	0.94[ASN][1000 genomes]
rs4571357	0.84[ASN][1000 genomes]
rs4577601	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4859509	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4859511	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4859875	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859877	0.82[ASW][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859888	0.88[ASN][1000 genomes]
rs4859889	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.85[ASN][1000 genomes]
rs6533282	0.85[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs6533291	0.94[ASN][1000 genomes]
rs6533344	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap]
rs6814912	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs6848029	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6854895	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7670157	0.81[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.84[MKK][hapmap];0.88[ASN][1000 genomes]
rs7675009	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.94[ASN][1000 genomes]
rs7676660	0.87[ASN][1000 genomes]
rs7698627	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829976	chr4:78576657-78757798	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4859879	MRPL1	cis	parietal	SCAN
rs4859879	MRPL1	cis	lymphoblastoid	seeQTL
rs4859879	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78716400-78733400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:78718200-78728200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:78718800-78738600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:78719200-78723200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:78720000-78723400	Enhancers	Psoas Muscle	Psoas
6	chr4:78720200-78722400	Weak transcription	GM12878-XiMat	blood
7	chr4:78720200-78723000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr4:78720200-78723200	Enhancers	Left Ventricle	heart
9	chr4:78720400-78724000	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr4:78720600-78722800	Weak transcription	Lung	lung
11	chr4:78720600-78723400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:78720600-78732000	Weak transcription	Aorta	Aorta
13	chr4:78720800-78735600	Weak transcription	HepG2	liver
14	chr4:78721000-78732400	Weak transcription	Fetal Intestine Small	intestine
15	chr4:78721200-78722400	Weak transcription	Dnd41	blood
16	chr4:78721200-78723200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr4:78721400-78722600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:78721400-78722800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr4:78721400-78722800	Enhancers	Brain Substantia Nigra	brain
20	chr4:78721400-78723000	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr4:78721400-78723000	Enhancers	Right Atrium	heart
22	chr4:78721400-78723200	Enhancers	Primary B cells from peripheral blood	blood
23	chr4:78721400-78723200	Enhancers	Small Intestine	intestine
24	chr4:78721400-78723600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:78721600-78722600	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr4:78721600-78722800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:78721600-78722800	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr4:78721600-78722800	Enhancers	Rectal Smooth Muscle	rectum
29	chr4:78721600-78723200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr4:78721800-78722400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr4:78721800-78722400	Enhancers	HMEC	breast
32	chr4:78721800-78722400	Enhancers	NH-A	brain
33	chr4:78721800-78722600	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr4:78721800-78722600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:78721800-78722600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:78721800-78722600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr4:78721800-78722600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr4:78721800-78722600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:78721800-78722600	Enhancers	Brain Cingulate Gyrus	brain
40	chr4:78721800-78722600	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr4:78721800-78722600	Enhancers	Fetal Lung	lung
42	chr4:78721800-78722600	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr4:78721800-78722600	Enhancers	A549	lung
44	chr4:78721800-78722800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr4:78721800-78722800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr4:78721800-78723400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr4:78721800-78724000	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr4:78721800-78724000	Enhancers	Primary hematopoietic stem cells	blood
49	chr4:78721800-78724400	Enhancers	Liver	Liver
50	chr4:78722000-78722400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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