Variant report

Variant	rs35001169
Chromosome Location	chr6:28187632-28187633
allele	G/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:33)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:33 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28184931..28189194-chr6:28190077..28194573,12	MCF-7	breast:
2	chr6:28184339..28187958-chr6:28190844..28194750,7	MCF-7	breast:
3	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
4	chr6:28108272..28111912-chr6:28184259..28187979,3	MCF-7	breast:
5	chr6:28187201..28188726-chr6:28351715..28353985,2	K562	blood:
6	chr6:28143030..28145517-chr6:28186267..28188999,2	K562	blood:
7	chr6:28186853..28189269-chr6:28360764..28363379,2	K562	blood:
8	chr6:28186992..28188596-chr6:28234642..28237014,2	K562	blood:
9	chr6:28184789..28191313-chr6:28230652..28235913,7	K562	blood:
10	chr6:28186460..28191177-chr6:28246836..28252039,7	K562	blood:
11	chr6:28081584..28085062-chr6:28187366..28190014,3	K562	blood:
12	chr6:28186877..28189778-chr6:28366321..28368559,2	K562	blood:
13	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
14	chr6:28100317..28107200-chr6:28184436..28191088,8	MCF-7	breast:
15	chr6:28187375..28189818-chr6:28709219..28712133,2	K562	blood:
16	chr6:28187353..28190192-chr6:28583076..28585455,2	K562	blood:
17	chr6:28102723..28113786-chr6:28183725..28194756,41	K562	blood:
18	chr6:28087049..28089835-chr6:28187380..28190025,2	K562	blood:
19	chr6:27857437..27861183-chr6:28187100..28189751,4	K562	blood:
20	chr6:28122601..28125129-chr6:28187296..28189318,2	K562	blood:
21	chr6:28135337..28137302-chr6:28186822..28190274,4	K562	blood:
22	chr6:28187278..28189645-chr6:28349848..28351599,2	K562	blood:
23	chr6:28187110..28190886-chr6:28224658..28229038,5	K562	blood:
24	chr6:27775362..27779371-chr6:28186093..28189957,4	K562	blood:
25	chr6:28114623..28117122-chr6:28187567..28190304,2	K562	blood:
26	chr6:28187359..28189911-chr6:28455377..28457870,2	K562	blood:
27	chr6:28184981..28190782-chr6:28297491..28307222,23	K562	blood:
28	chr6:28103775..28113920-chr6:28177995..28190115,32	K562	blood:
29	chr6:28130769..28134274-chr6:28187281..28190236,3	K562	blood:
30	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:
31	chr6:28187117..28189206-chr6:28783315..28785702,2	K562	blood:
32	chr6:27856777..27859583-chr6:28186890..28189718,3	K562	blood:
33	chr6:27860430..27862717-chr6:28186992..28190210,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000158691	Chromatin interaction
ENSG00000216901	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000219392	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000232040	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000189134	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs13190888	0.88[EUR][1000 genomes]
rs13191786	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13195291	1.00[EUR][1000 genomes]
rs13197574	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13197633	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13198809	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13200214	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13201308	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13201681	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13203816	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13204012	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13205211	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13205911	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13207345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13208096	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13211507	0.93[EUR][1000 genomes]
rs13213152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13213986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13214023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13217619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13217984	0.93[EUR][1000 genomes]
rs2232423	0.89[EUR][1000 genomes]
rs2232426	0.89[EUR][1000 genomes]
rs2232429	0.89[EUR][1000 genomes]
rs33932084	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34166054	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34218844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34243448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34371502	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34396849	0.93[EUR][1000 genomes]
rs34505829	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34546986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34588114	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34661125	0.93[EUR][1000 genomes]
rs34691223	0.93[EUR][1000 genomes]
rs34765154	0.93[EUR][1000 genomes]
rs34832585	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34871267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34878803	0.93[EUR][1000 genomes]
rs34950484	0.93[EUR][1000 genomes]
rs35016036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35017208	0.93[EUR][1000 genomes]
rs35030260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35072899	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35098436	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs35345226	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs35353359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35656932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35744819	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35749575	0.93[EUR][1000 genomes]
rs35781323	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs35883476	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35902873	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs35952432	0.83[EUR][1000 genomes]
rs36092177	0.89[EUR][1000 genomes]
rs56075693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56189111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66886492	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs67297533	0.89[EUR][1000 genomes]
rs67340775	0.91[EUR][1000 genomes]
rs67381177	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67981811	0.89[EUR][1000 genomes]
rs67998226	0.93[EUR][1000 genomes]
rs68188794	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs71537572	1.00[AFR][1000 genomes]
rs71559070	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs71559072	0.93[EUR][1000 genomes]
rs72846780	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs72846794	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs72854513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35001169	AL022393.7	cis	Muscle Skeletal	GTEx
rs35001169	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs35001169	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs35001169	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28186600-28192400	Weak transcription	Spleen	Spleen
2	chr6:28187000-28188000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:28187000-28188000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:28187000-28188200	Weak transcription	NH-A	brain
5	chr6:28187000-28188600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:28187000-28192400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:28187000-28192400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:28187200-28188200	Enhancers	Placenta	Placenta
9	chr6:28187200-28189800	Weak transcription	NHEK	skin
10	chr6:28187200-28190800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:28187200-28192000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:28187200-28192000	Weak transcription	HMEC	breast
13	chr6:28187200-28192200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:28187400-28188000	Enhancers	HepG2	liver
15	chr6:28187400-28192000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:28187400-28192000	Weak transcription	Hela-S3	cervix
17	chr6:28187600-28187800	Enhancers	K562	blood

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