Variant report

Variant	rs263178
Chromosome Location	chr6:142865106-142865107
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1040525	0.82[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs1040526	0.87[EUR][1000 genomes]
rs1360194	0.83[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs155259	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294764	0.88[EUR][1000 genomes]
rs2294771	0.87[EUR][1000 genomes]
rs262115	0.87[EUR][1000 genomes]
rs262119	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs262121	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs262129	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs263179	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs263180	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263181	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263182	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263184	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263185	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs263186	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263187	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263188	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs263189	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3748069	0.87[EUR][1000 genomes]
rs3817929	0.87[EUR][1000 genomes]
rs611802	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6570507	0.88[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs6570509	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs6570510	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs6909857	0.84[EUR][1000 genomes]
rs6929442	0.87[EUR][1000 genomes]
rs6937121	0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs7753012	0.83[TSI][hapmap]
rs7754638	0.87[EUR][1000 genomes]
rs7755109	0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs7756305	0.83[TSI][hapmap]
rs7763064	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7770386	0.86[EUR][1000 genomes]
rs7774095	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs7776375	0.86[EUR][1000 genomes]
rs9373346	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs9389986	0.81[EUR][1000 genomes]
rs9403382	0.82[EUR][1000 genomes]
rs9403383	0.83[CEU][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs9403387	0.88[EUR][1000 genomes]
rs9496346	0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs9496369	0.85[EUR][1000 genomes]
rs9496374	0.86[EUR][1000 genomes]
rs9496392	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs962554	0.86[EUR][1000 genomes]
rs972982	0.86[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS 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 miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1023426	chr6:142813845-142940262	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830827	chr6:142840734-143015005	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142846600-142865600	Weak transcription	Right Atrium	heart
2	chr6:142864000-142865800	Enhancers	Primary T cells from cord blood	blood
3	chr6:142864200-142865200	Enhancers	Fetal Lung	lung
4	chr6:142864400-142865400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:142864400-142869400	Weak transcription	HMEC	breast
6	chr6:142864400-142871800	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:142864400-142872000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:142864400-142872000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:142864400-142872000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:142864400-142872200	Weak transcription	NHEK	skin
11	chr6:142864800-142866800	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr6:142864800-142867000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr6:142864800-142867400	Enhancers	Dnd41	blood
14	chr6:142865000-142865800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:142865000-142866800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr6:142865000-142867000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr6:142865000-142867000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr6:142865000-142867200	Enhancers	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links