Variant report

Variant	rs16889690
Chromosome Location	chr6:34383788-34383789
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:34194332..34197149-chr6:34382426..34385429,3	K562	blood:
2	chr6:34382272..34384689-chr6:34494911..34496600,2	K562	blood:
3	chr6:34216446..34218466-chr6:34382282..34384611,2	MCF-7	breast:
4	chr6:34206861..34220421-chr6:34379359..34386848,24	K562	blood:
5	chr6:34164046..34167260-chr6:34381691..34384552,3	K562	blood:
6	chr6:34209557..34211500-chr6:34382347..34384028,2	K562	blood:
7	chr6:34210046..34211702-chr6:34381668..34384170,2	MCF-7	breast:
8	chr6:34356693..34361584-chr6:34376924..34385699,12	K562	blood:
9	chr6:34212124..34218246-chr6:34379945..34387655,19	K562	blood:
10	chr6:34161815..34164629-chr6:34383451..34385385,2	MCF-7	breast:
11	chr6:34358383..34362134-chr6:34382278..34385330,4	K562	blood:
12	chr6:34382616..34385085-chr6:34576008..34577878,2	K562	blood:
13	chr6:34381801..34383891-chr6:34543770..34545644,2	K562	blood:
14	chr6:34162021..34165758-chr6:34380623..34387316,6	K562	blood:
15	chr6:34202204..34208226-chr6:34378240..34384748,6	K562	blood:
16	chr6:34197271..34199519-chr6:34383050..34384850,2	K562	blood:
17	chr6:34236991..34239302-chr6:34382683..34384856,2	K562	blood:
18	chr6:34216483..34218885-chr6:34383067..34384781,3	MCF-7	breast:
19	chr6:34218726..34220421-chr6:34383770..34386594,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196114	Chromatin interaction
ENSG00000272325	Chromatin interaction
ENSG00000186577	Chromatin interaction
ENSG00000137309	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10452589	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16885036	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs16889678	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16889754	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[EUR][1000 genomes]
rs16889851	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2894394	1.00[CEU][hapmap]
rs56022767	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58211939	0.85[EUR][1000 genomes]
rs58525086	0.84[EUR][1000 genomes]
rs59368811	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60208416	0.84[EUR][1000 genomes]
rs60708749	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61618829	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62399910	0.84[EUR][1000 genomes]
rs62399912	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62399914	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62399917	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62399919	0.84[EUR][1000 genomes]
rs62399946	0.84[EUR][1000 genomes]
rs62399947	0.84[EUR][1000 genomes]
rs6906664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6908522	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs73403917	0.85[EUR][1000 genomes]
rs73403918	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs73403996	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73405614	0.84[EUR][1000 genomes]
rs7741867	0.84[EUR][1000 genomes]
rs7742115	0.84[EUR][1000 genomes]
rs7760471	0.84[EUR][1000 genomes]
rs9380430	1.00[CEU][hapmap];1.00[GIH][hapmap]

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	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16889690	PRELP	trans	brain	seeQTL
rs16889690	TMEM30B	trans	brain	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34361000-34384800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:34361200-34384800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:34371400-34384000	Weak transcription	Right Ventricle	heart
4	chr6:34372400-34389400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:34377200-34384800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:34377400-34383800	Weak transcription	Esophagus	oesophagus
7	chr6:34377400-34385000	Weak transcription	Psoas Muscle	Psoas
8	chr6:34378600-34383800	Weak transcription	Left Ventricle	heart
9	chr6:34378800-34383800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:34378800-34383800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:34378800-34385000	Weak transcription	Aorta	Aorta
12	chr6:34379000-34383800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:34379000-34383800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr6:34379200-34384800	Weak transcription	Hela-S3	cervix
15	chr6:34379200-34384800	Weak transcription	HSMMtube	muscle
16	chr6:34379200-34385400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr6:34379200-34391800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:34379400-34383800	Weak transcription	Primary B cells from cord blood	blood
19	chr6:34379400-34384600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:34379600-34383800	Weak transcription	NHLF	lung
21	chr6:34380200-34384800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:34380800-34383800	Weak transcription	HSMM	muscle
23	chr6:34381000-34383800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:34381000-34384000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:34381000-34384000	Weak transcription	NH-A	brain
26	chr6:34381200-34383800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:34381200-34383800	Weak transcription	HMEC	breast
28	chr6:34381400-34383800	Weak transcription	HUVEC	blood vessel
29	chr6:34381800-34391000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:34382000-34383800	Enhancers	Liver	Liver
31	chr6:34382000-34384000	Strong transcription	A549	lung
32	chr6:34382000-34384600	Enhancers	Stomach Mucosa	stomach
33	chr6:34382000-34388000	Strong transcription	Dnd41	blood
34	chr6:34382000-34390000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:34382000-34391600	Strong transcription	NHEK	skin
36	chr6:34382000-34392000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:34382000-34392000	Strong transcription	Primary T cells from cord blood	blood
38	chr6:34382200-34383800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:34382400-34384000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:34382400-34384000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr6:34382400-34384000	Enhancers	Pancreas	Pancrea
42	chr6:34382400-34384000	Weak transcription	Spleen	Spleen
43	chr6:34382400-34389400	Strong transcription	K562	blood
44	chr6:34382400-34389600	Weak transcription	Fetal Brain Male	brain
45	chr6:34382400-34391800	Strong transcription	NHDF-Ad	bronchial
46	chr6:34382400-34392000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr6:34382400-34392000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:34382400-34392000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:34382600-34384000	Weak transcription	Gastric	stomach
50	chr6:34382600-34384600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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