Variant report

Variant	rs12660916
Chromosome Location	chr6:36874428-36874429
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36872618..36878206-chr6:36882033..36886554,6	K562	blood:
2	chr6:36871983..36875011-chr6:36953763..36955821,3	MCF-7	breast:
3	chr6:36872207..36874617-chr6:36875523..36877749,2	MCF-7	breast:
4	chr6:36873455..36875105-chr6:36887491..36889337,2	K562	blood:
5	chr6:36841707..36844082-chr6:36873822..36876086,2	K562	blood:
6	chr6:36853581..36857418-chr6:36873460..36876279,5	K562	blood:
7	chr6:36868611..36871179-chr6:36873388..36875751,3	K562	blood:
8	chr6:36873016..36874833-chr6:36874894..36877629,2	K562	blood:
9	chr6:36865210..36867314-chr6:36872831..36875830,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000137168	Chromatin interaction
ENSG00000198663	Chromatin interaction
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10947649	1.00[CEU][hapmap]
rs11542163	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751310	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751956	1.00[CEU][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753183	0.88[EUR][1000 genomes]
rs11753835	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11757851	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11759158	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11759163	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12660989	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191679	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192293	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200132	1.00[ASN][1000 genomes]
rs13205108	0.88[EUR][1000 genomes]
rs13205292	1.00[CEU][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206310	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207209	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210299	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13219894	0.80[CEU][hapmap]
rs13219913	0.80[CEU][hapmap]
rs17552005	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]
rs34405617	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34433592	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34510528	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34597881	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34869908	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34913693	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35819257	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36098393	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71569352	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71569356	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470425	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][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
rs12660916	C6orf89	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36854200-36881000	Weak transcription	Gastric	stomach
2	chr6:36854200-36887400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:36854400-36893000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:36854800-36875200	Weak transcription	Esophagus	oesophagus
5	chr6:36854800-36881000	Weak transcription	A549	lung
6	chr6:36854800-36882000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:36854800-36884600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:36855400-36881000	Weak transcription	Small Intestine	intestine
9	chr6:36859600-36879400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr6:36861200-36879000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr6:36862000-36875800	Strong transcription	Dnd41	blood
12	chr6:36864600-36881200	Strong transcription	Fetal Intestine Small	intestine
13	chr6:36865400-36876600	Strong transcription	Duodenum Mucosa	Duodenum
14	chr6:36866000-36875800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:36866000-36876800	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:36866000-36877200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:36866200-36876800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:36866200-36877600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr6:36866200-36878400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:36866200-36896400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr6:36866400-36877800	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:36866600-36876000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:36866600-36876200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:36866600-36878400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr6:36866600-36878400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:36866800-36876000	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr6:36866800-36881600	Strong transcription	Fetal Intestine Large	intestine
28	chr6:36867000-36897000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:36868600-36882000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:36869600-36874800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:36869600-36875600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:36869600-36875600	Strong transcription	Placenta	Placenta
33	chr6:36869600-36876800	Strong transcription	Adipose Nuclei	Adipose
34	chr6:36869600-36877400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr6:36869800-36874800	Strong transcription	K562	blood
36	chr6:36869800-36875200	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr6:36869800-36876000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:36869800-36878400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:36869800-36881400	Strong transcription	HepG2	liver
40	chr6:36870600-36875600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:36870600-36882000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr6:36870600-36882000	Weak transcription	Fetal Kidney	kidney
43	chr6:36870800-36889400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:36871000-36875600	Weak transcription	Psoas Muscle	Psoas
45	chr6:36871000-36879400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr6:36871000-36879800	Weak transcription	HMEC	breast
47	chr6:36871000-36888400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:36871200-36882000	Weak transcription	Hela-S3	cervix
49	chr6:36871400-36876800	Genic enhancers	Fetal Thymus	thymus
50	chr6:36871600-36876800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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