Variant report

Variant	rs6864647
Chromosome Location	chr5:112263966-112263967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112257473..112261765-chr5:112262739..112268514,7	K562	blood:
2	chr5:112255808..112259712-chr5:112262639..112265626,6	MCF-7	breast:
3	chr5:112263017..112264947-chr5:112304699..112307617,2	MCF-7	breast:
4	chr5:112254019..112256413-chr5:112263500..112265377,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129625	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10064080	0.83[ASN][1000 genomes]
rs10519333	0.81[CHB][hapmap]
rs13354064	0.82[ASN][1000 genomes]
rs13360667	0.83[ASN][1000 genomes]
rs17135070	0.82[CHB][hapmap]
rs17135100	0.82[CHB][hapmap]
rs17135149	0.82[CHB][hapmap]
rs17135155	0.82[CHB][hapmap]
rs17135193	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];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17370550	0.82[EUR][1000 genomes]
rs17371015	0.82[EUR][1000 genomes]
rs1833560	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28635838	0.81[ASN][1000 genomes]
rs28789211	0.83[ASN][1000 genomes]
rs3733963	0.82[CHB][hapmap]
rs3822654	0.82[CHB][hapmap]
rs3892986	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3962814	0.86[ASN][1000 genomes]
rs55771309	0.94[EUR][1000 genomes]
rs56155803	0.94[EUR][1000 genomes]
rs56321569	0.82[EUR][1000 genomes]
rs57749964	0.93[ASN][1000 genomes]
rs58775131	0.91[ASN][1000 genomes]
rs59349522	0.98[ASN][1000 genomes]
rs6594652	0.82[CHB][hapmap]
rs6864403	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs728344	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[ASN][1000 genomes]
rs728347	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs73227370	0.90[ASN][1000 genomes]
rs73227382	0.93[ASN][1000 genomes]
rs73227383	0.89[ASN][1000 genomes]
rs7728481	0.84[CHB][hapmap]
rs7728766	0.82[EUR][1000 genomes]
rs7730241	0.91[ASN][1000 genomes]
rs7730441	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7735121	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	esv2763866	chr5:112254282-112284223	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6864647	ABCB9	trans	lymphoblastoid	seeQTL
rs6864647	REEP5	cis	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112258000-112265000	Weak transcription	Small Intestine	intestine
2	chr5:112258400-112287400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:112258600-112264000	Weak transcription	A549	lung
4	chr5:112258600-112264200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:112259000-112267200	Weak transcription	Psoas Muscle	Psoas
6	chr5:112259000-112267200	Weak transcription	Right Atrium	heart
7	chr5:112259000-112269200	Weak transcription	Osteobl	bone
8	chr5:112259400-112264000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:112259600-112265000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:112259600-112267600	Enhancers	Primary B cells from peripheral blood	blood
11	chr5:112259800-112265200	Enhancers	Primary B cells from cord blood	blood
12	chr5:112260200-112264000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr5:112260400-112267000	Weak transcription	K562	blood
14	chr5:112262200-112266000	Flanking Active TSS	GM12878-XiMat	blood
15	chr5:112262400-112265600	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr5:112262400-112267400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:112262400-112267600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr5:112262400-112267800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr5:112262600-112265000	Enhancers	Primary T cells from cord blood	blood
20	chr5:112262600-112265000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:112262600-112265200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr5:112262600-112267600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:112262800-112265000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr5:112263000-112264000	Weak transcription	Fetal Brain Male	brain
25	chr5:112263000-112266000	Enhancers	Placenta	Placenta
26	chr5:112263000-112267400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr5:112263200-112265000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr5:112263200-112266800	Enhancers	Dnd41	blood
29	chr5:112263200-112267600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:112263200-112268200	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr5:112263400-112264400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:112263400-112264400	Enhancers	Hela-S3	cervix
33	chr5:112263400-112265000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr5:112263400-112265200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr5:112263400-112266600	Enhancers	Primary hematopoietic stem cells	blood
36	chr5:112263400-112267400	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr5:112263600-112267400	Enhancers	Fetal Thymus	thymus
38	chr5:112263800-112264200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr5:112263800-112264400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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