Variant report

Variant	rs13217620
Chromosome Location	chr6:27653120-27653121
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27649669..27653830-chr6:27777087..27779964,4	K562	blood:
2	chr6:27651512..27653826-chr6:27705257..27706833,2	MCF-7	breast:
3	chr6:26157709..26160527-chr6:27652388..27654898,2	MCF-7	breast:
4	chr6:27635489..27641593-chr6:27648456..27655439,10	K562	blood:
5	chr6:27651230..27653525-chr6:27660393..27663354,2	MCF-7	breast:
6	chr6:27638297..27640693-chr6:27651718..27653720,2	MCF-7	breast:
7	chr6:27644939..27650269-chr6:27651814..27657274,7	K562	blood:
8	chr6:27642885..27644843-chr6:27650886..27653382,2	K562	blood:
9	chr6:27652252..27653760-chr6:27657291..27659495,2	MCF-7	breast:
10	chr6:27651170..27656145-chr6:27660253..27663653,4	MCF-7	breast:
11	chr6:27652290..27655444-chr6:27857919..27861967,3	K562	blood:
12	chr6:27598559..27601454-chr6:27650753..27653597,2	K562	blood:
13	chr6:27652463..27655224-chr6:27720018..27721922,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000216915	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000238648	Chromatin interaction
ENSG00000203813	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10484399	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13192965	1.00[EUR][1000 genomes]
rs13193480	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13193542	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13194781	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13195636	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13195728	0.87[EUR][1000 genomes]
rs13199649	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13199772	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13199906	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13202291	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13202295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13202775	0.92[EUR][1000 genomes]
rs13209332	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13210634	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13212318	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs13212651	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13215275	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs175597	0.91[CEU][hapmap]
rs17693963	1.00[CEU][hapmap]
rs17695758	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17749927	1.00[EUR][1000 genomes]
rs17750747	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs17751184	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17763089	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs200481	0.91[CEU][hapmap]
rs200482	0.91[CEU][hapmap]
rs200483	0.91[CEU][hapmap]
rs200484	0.91[CEU][hapmap]
rs200485	0.91[CEU][hapmap]
rs200490	0.91[CEU][hapmap]
rs200501	0.91[CEU][hapmap]
rs200948	0.91[CEU][hapmap]
rs200949	0.91[CEU][hapmap]
rs200953	0.91[CEU][hapmap]
rs200954	0.91[CEU][hapmap]
rs200981	0.89[CEU][hapmap]
rs200989	0.91[CEU][hapmap]
rs200990	0.91[CEU][hapmap]
rs200995	0.91[CEU][hapmap]
rs201002	0.91[CEU][hapmap]
rs2747054	0.91[CEU][hapmap]
rs34064842	0.98[EUR][1000 genomes]
rs34105070	0.92[EUR][1000 genomes]
rs34194357	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs34409918	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs34432857	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs34573979	0.81[EUR][1000 genomes]
rs34706883	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs34718920	0.87[EUR][1000 genomes]
rs34965299	0.85[EUR][1000 genomes]
rs35037868	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35202262	1.00[AFR][1000 genomes]
rs35339855	1.00[AFR][1000 genomes]
rs35501037	0.94[EUR][1000 genomes]
rs35715914	1.00[EUR][1000 genomes]
rs35819751	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35848276	0.85[EUR][1000 genomes]
rs36116761	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs370155	0.91[CEU][hapmap]
rs401763	0.91[CEU][hapmap]
rs425335	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs45509595	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs56405707	1.00[EUR][1000 genomes]
rs58616630	0.81[EUR][1000 genomes]
rs66785117	0.85[EUR][1000 genomes]
rs66868086	0.83[EUR][1000 genomes]
rs67101035	0.87[EUR][1000 genomes]
rs67652222	0.98[EUR][1000 genomes]
rs71559038	0.98[EUR][1000 genomes]
rs71559050	0.87[EUR][1000 genomes]
rs72845046	0.98[EUR][1000 genomes]
rs72845070	1.00[EUR][1000 genomes]
rs72847313	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv1023673	chr6:27570731-27688782	Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
5	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv525669	chr6:27623511-27657647	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv883511	chr6:27623511-27660508	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	esv2830157	chr6:27634640-27657647	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv518945	chr6:27634640-27668013	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13217620	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs13217620	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13217620	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27649200-27654600	Weak transcription	NHEK	skin
2	chr6:27649200-27655000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:27652200-27655000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:27652200-27655000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:27652400-27654800	Weak transcription	Hela-S3	cervix
6	chr6:27652400-27655000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:27652400-27655000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:27652400-27655000	Weak transcription	GM12878-XiMat	blood
9	chr6:27652600-27653400	Enhancers	Primary T cells fromperipheralblood	blood
10	chr6:27652600-27655000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr6:27652800-27653600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:27652800-27653800	Enhancers	HepG2	liver
13	chr6:27652800-27654200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr6:27652800-27654600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:27652800-27654800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr6:27652800-27654800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:27652800-27654800	Weak transcription	A549	lung
18	chr6:27652800-27654800	Weak transcription	K562	blood
19	chr6:27652800-27655000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr6:27653000-27655000	Weak transcription	Right Atrium	heart

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