Variant report

Variant	rs17552005
Chromosome Location	chr6:36841830-36841831
allele	A/C/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36807524..36809361-chr6:36841077..36843091,2	K562	blood:
2	chr6:36733877..36734566-chr6:36841546..36842101,2	MCF-7	breast:
3	chr6:36840111..36842444-chr6:37018601..37020201,2	MCF-7	breast:
4	chr6:36839698..36842485-chr6:36952323..36954016,2	K562	blood:
5	chr6:36841771..36843991-chr6:36852556..36855136,3	MCF-7	breast:
6	chr6:36841338..36845965-chr6:36851992..36855231,4	MCF-7	breast:
7	chr6:36838369..36843263-chr6:36951921..36955568,5	MCF-7	breast:
8	chr6:36561980..36564185-chr6:36840792..36844090,3	K562	blood:
9	chr6:36735629..36738074-chr6:36841042..36842717,2	K562	blood:
10	chr6:36807086..36809328-chr6:36841078..36843476,3	K562	blood:
11	chr6:36562065..36563624-chr6:36841124..36842701,2	K562	blood:
12	chr6:36841093..36843369-chr6:37223969..37226953,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198663	Chromatin interaction
ENSG00000112081	Chromatin interaction
ENSG00000124772	Chromatin interaction
ENSG00000172738	Chromatin interaction
ENSG00000065491	Chromatin interaction
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10947649	1.00[CEU][hapmap]
rs11542163	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751310	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751956	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753183	0.81[EUR][1000 genomes]
rs11753835	0.95[AMR][1000 genomes]
rs11757851	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11759158	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11759163	0.81[EUR][1000 genomes]
rs12660916	1.00[CEU][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660989	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191679	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192293	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200132	1.00[ASN][1000 genomes]
rs13205108	0.81[EUR][1000 genomes]
rs13205292	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207209	1.00[CEU][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210299	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219894	0.80[CEU][hapmap]
rs13219913	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs34405617	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34433592	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34510528	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34597881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34869908	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34913693	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35819257	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36098393	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71569352	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71569356	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470425	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470429	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17552005	C6orf89	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36817200-36842000	Weak transcription	Stomach Mucosa	stomach
2	chr6:36832200-36842000	Weak transcription	Aorta	Aorta
3	chr6:36835600-36842000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:36835600-36842000	Weak transcription	Lung	lung
5	chr6:36837000-36842200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:36840400-36842200	Enhancers	Spleen	Spleen
7	chr6:36841000-36843200	Active TSS	GM12878-XiMat	blood
8	chr6:36841200-36842000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr6:36841200-36842000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:36841200-36842200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:36841200-36843200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:36841400-36842000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:36841400-36842000	Enhancers	Primary B cells from peripheral blood	blood
14	chr6:36841400-36842000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:36841400-36842000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:36841400-36842000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr6:36841400-36842000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr6:36841400-36842000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
19	chr6:36841400-36842000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr6:36841400-36842000	Flanking Active TSS	Fetal Lung	lung
21	chr6:36841400-36842000	Flanking Active TSS	Right Ventricle	heart
22	chr6:36841400-36842000	Flanking Active TSS	Hela-S3	cervix
23	chr6:36841400-36842000	Flanking Active TSS	HSMM	muscle
24	chr6:36841400-36842000	Flanking Active TSS	HSMMtube	muscle
25	chr6:36841400-36842000	Flanking Active TSS	HUVEC	blood vessel
26	chr6:36841400-36842000	Flanking Active TSS	NH-A	brain
27	chr6:36841400-36842000	Flanking Active TSS	NHEK	skin
28	chr6:36841400-36842000	Flanking Active TSS	NHLF	lung
29	chr6:36841400-36842000	Flanking Active TSS	Osteobl	bone
30	chr6:36841400-36842200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:36841400-36842200	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr6:36841400-36842200	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr6:36841400-36842200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr6:36841400-36842200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr6:36841400-36842200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr6:36841400-36842200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:36841400-36842200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:36841400-36842200	Flanking Active TSS	Liver	Liver
39	chr6:36841400-36842200	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr6:36841400-36842200	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr6:36841400-36842200	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr6:36841400-36842200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr6:36841400-36842400	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr6:36841400-36842400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr6:36841400-36843200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:36841400-36843200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:36841400-36843400	Active TSS	H9 Cell Line	embryonic stem cell
48	chr6:36841400-36843400	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr6:36841400-36843400	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr6:36841600-36842000	Flanking Active TSS	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links