Variant report

Variant	rs558627
Chromosome Location	chr6:163519903-163519904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs2763991	0.85[EUR][1000 genomes]
rs2985041	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs472033	0.89[ASN][1000 genomes]
rs476062	0.93[ASN][1000 genomes]
rs476445	0.85[EUR][1000 genomes]
rs477514	0.89[ASN][1000 genomes]
rs477618	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs480064	0.94[EUR][1000 genomes]
rs488831	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs498325	0.87[ASN][1000 genomes]
rs500019	0.90[ASN][1000 genomes]
rs501775	0.90[ASN][1000 genomes]
rs510791	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs520847	0.82[EUR][1000 genomes]
rs522682	0.82[EUR][1000 genomes]
rs524763	0.87[EUR][1000 genomes]
rs528064	0.94[ASN][1000 genomes]
rs532764	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs535238	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs536392	0.87[ASN][1000 genomes]
rs537327	0.87[ASN][1000 genomes]
rs542711	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs547244	0.92[ASN][1000 genomes]
rs54773	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs548705	0.90[EUR][1000 genomes]
rs551705	0.92[ASN][1000 genomes]
rs551797	0.94[EUR][1000 genomes]
rs552752	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs554159	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs561216	0.95[ASN][1000 genomes]
rs562100	0.95[ASN][1000 genomes]
rs568619	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs570398	0.90[ASN][1000 genomes]
rs573070	0.93[ASN][1000 genomes]
rs576381	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs578822	0.94[ASN][1000 genomes]
rs578974	0.87[ASN][1000 genomes]
rs579172	0.94[EUR][1000 genomes]
rs579628	0.92[ASN][1000 genomes]
rs579982	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917926	chr6:162646457-163609259	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1026490	chr6:163133433-163705708	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv869286	chr6:163146342-163697445	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1030116	chr6:163273707-163525678	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv916587	chr6:163337791-163606120	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv886917	chr6:163507051-163573962	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163508800-163520800	Weak transcription	Pancreas	Pancrea
2	chr6:163515000-163520000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:163515200-163520000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:163515600-163520200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:163516400-163520000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:163516400-163520200	Weak transcription	Fetal Brain Male	brain
7	chr6:163519200-163520600	Enhancers	Brain Cingulate Gyrus	brain
8	chr6:163519200-163520600	Enhancers	Brain Substantia Nigra	brain
9	chr6:163519200-163521200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:163519400-163520200	Enhancers	Brain Anterior Caudate	brain
11	chr6:163519400-163520200	Enhancers	Brain Hippocampus Middle	brain
12	chr6:163519400-163520800	Enhancers	Fetal Heart	heart
13	chr6:163519400-163521600	Enhancers	Brain Germinal Matrix	brain
14	chr6:163519600-163520000	Weak transcription	Left Ventricle	heart
15	chr6:163519600-163520200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:163519600-163520200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:163519600-163520200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:163519600-163520600	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr6:163519600-163521200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:163519800-163521000	Enhancers	Right Ventricle	heart

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