Variant report

Variant	rs6098158
Chromosome Location	chr20:53297972-53297973
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:37)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:37 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:53297245..53298058-chr3:64752403..64753296,2	MCF-7	breast:
2	chr20:53284764..53285373-chr20:53297635..53298458,2	MCF-7	breast:
3	chr1:61620670..61621170-chr20:53297255..53298211,4	MCF-7	breast:
4	chr20:53297140..53298069-chr20:54745859..54746826,6	MCF-7	breast:
5	chr20:53296558..53298632-chr3:64515452..64516902,29	MCF-7	breast:
6	chr20:53297392..53298300-chr3:64657661..64658275,2	MCF-7	breast:
7	chr20:53294274..53296254-chr20:53296968..53298496,2	MCF-7	breast:
8	chr20:52559737..52560546-chr20:53297221..53297991,3	MCF-7	breast:
9	chr20:52559479..52560840-chr20:53297067..53298188,6	MCF-7	breast:
10	chr17:62396854..62397477-chr20:53297283..53297991,2	MCF-7	breast:
11	chr20:53296906..53298947-chr20:53330986..53333656,2	MCF-7	breast:
12	chr20:53264760..53267099-chr20:53297639..53299981,2	MCF-7	breast:
13	chr20:53297756..53299793-chr20:53421394..53423179,2	MCF-7	breast:
14	chr20:53297100..53298020-chr20:54756384..54757317,8	MCF-7	breast:
15	chr2:180091649..180092168-chr20:53297444..53298069,2	MCF-7	breast:
16	chr20:53297077..53298037-chr3:64523265..64523990,2	MCF-7	breast:
17	chr20:53297044..53298391-chr20:53342876..53343999,9	MCF-7	breast:
18	chr20:53296415..53300428-chr3:64512136..64516086,4	MCF-7	breast:
19	chr20:53297064..53298077-chr3:64515896..64517016,10	MCF-7	breast:
20	chr20:53297072..53298027-chr20:54824104..54825055,3	K562	blood:
21	chr20:53297141..53300024-chr20:53303959..53305467,2	MCF-7	breast:
22	chr20:53295710..53298032-chr3:64518048..64519638,2	MCF-7	breast:
23	chr20:53297063..53298490-chr3:64703588..64704964,7	MCF-7	breast:
24	chr20:53296962..53298212-chr3:62618518..62619402,4	MCF-7	breast:
25	chr20:53297030..53299399-chr3:64518913..64520051,28	MCF-7	breast:
26	chr20:53296950..53299252-chr3:64517666..64520403,2	MCF-7	breast:
27	chr12:78539699..78540376-chr20:53297270..53297982,2	MCF-7	breast:
28	chr20:53296551..53298207-chr20:53342710..53343895,13	MCF-7	breast:
29	chr20:53265389..53267623-chr20:53296471..53298044,17	MCF-7	breast:
30	chr20:53296916..53298758-chr3:64518136..64520683,88	MCF-7	breast:
31	chr20:53293305..53299094-chr20:53306694..53312269,5	MCF-7	breast:
32	chr20:46292642..46293430-chr20:53297468..53297992,2	MCF-7	breast:
33	chr20:53297230..53298183-chr3:64015995..64017242,8	MCF-7	breast:
34	chr17:62397987..62399090-chr20:53297150..53298132,13	MCF-7	breast:
35	chr20:52556178..52557055-chr20:53297089..53298051,7	MCF-7	breast:
36	chr20:52556090..52556889-chr20:53296922..53298074,4	MCF-7	breast:
37	chr20:53297545..53298234-chr3:64561557..64562303,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236352	Chromatin interaction
ENSG00000163638	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1013660	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13040265	1.00[CHD][hapmap]
rs1569985	1.00[CHD][hapmap]
rs1983702	1.00[CHD][hapmap]
rs2180462	1.00[CHD][hapmap]
rs2208075	1.00[CHD][hapmap]
rs2224269	1.00[CHD][hapmap]
rs2870333	1.00[CHD][hapmap]
rs2870337	1.00[CHD][hapmap]
rs2870347	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4302265	1.00[CHD][hapmap]
rs4334548	1.00[CHD][hapmap]
rs4809969	1.00[CHD][hapmap]
rs6014081	1.00[CHD][hapmap]
rs6014106	1.00[CHD][hapmap]
rs6014127	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6014128	1.00[CEU][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6014130	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023367	1.00[CHD][hapmap]
rs6023406	1.00[CHD][hapmap]
rs6023423	1.00[CHD][hapmap]
rs6023429	1.00[CHD][hapmap]
rs6023430	1.00[CHD][hapmap]
rs6023474	1.00[CHD][hapmap];0.89[GIH][hapmap]
rs6023481	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6023500	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6064093	1.00[CHD][hapmap]
rs6064102	1.00[CHD][hapmap];0.89[GIH][hapmap]
rs6068924	1.00[CHD][hapmap]
rs6091947	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6098108	1.00[CHD][hapmap]
rs6123404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7263678	1.00[CHD][hapmap]
rs7270451	1.00[CHD][hapmap]
rs7270971	1.00[CHD][hapmap]
rs8115071	1.00[CHD][hapmap]
rs8124702	1.00[CHD][hapmap]
rs910850	1.00[CHD][hapmap]
rs966548	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs967377	1.00[CHD][hapmap]
rs993806	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs993807	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]

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	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
2	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv1060552	chr20:53234716-53655115	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv586283	chr20:53288595-53311415	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6098158	CX3CL1	trans	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53296800-53299600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr20:53297000-53298200	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr20:53297000-53298200	Enhancers	Colon Smooth Muscle	Colon
4	chr20:53297000-53298600	Enhancers	Duodenum Smooth Muscle	Duodenum
5	chr20:53297000-53299200	Enhancers	Brain Germinal Matrix	brain
6	chr20:53297200-53298200	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr20:53297200-53298200	Enhancers	Rectal Smooth Muscle	rectum
8	chr20:53297200-53298600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr20:53297200-53298600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr20:53297200-53298800	Enhancers	Fetal Brain Female	brain
11	chr20:53297200-53299000	Enhancers	Stomach Smooth Muscle	stomach
12	chr20:53297200-53299600	Enhancers	Fetal Stomach	stomach
13	chr20:53297400-53298200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr20:53297600-53298400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr20:53297600-53298600	Enhancers	Adipose Nuclei	Adipose
16	chr20:53297600-53298800	Enhancers	Fetal Lung	lung
17	chr20:53297600-53299000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr20:53297600-53299200	Enhancers	Fetal Brain Male	brain
19	chr20:53297800-53298600	Enhancers	Fetal Muscle Leg	muscle

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