Variant report

Variant	rs9364689
Chromosome Location	chr6:163929340-163929341
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163921298..163924177-chr6:163927731..163929828,2	MCF-7	breast:
2	chr6:163926892..163930001-chr6:163930926..163934200,4	K562	blood:
3	chr6:163923513..163926538-chr6:163926650..163930288,4	K562	blood:
4	chr6:163927892..163930001-chr6:163930926..163932933,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL078585.1-4	chr6:163928265-163929595	ENSG00000251068

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1047935	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11962088	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs13199835	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13202282	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16895015	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1737328	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs17591955	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs2143358	0.83[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2294698	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2294703	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2294706	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294707	0.82[ASN][1000 genomes]
rs2294709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35442073	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3756879	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs3763197	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4263561	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs4709716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4709717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4709718	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4709720	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4709722	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59759961	0.83[ASN][1000 genomes]
rs6455897	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs6931903	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6939218	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs715020	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs724826	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73015387	0.80[ASN][1000 genomes]
rs7758706	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs7772756	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs9346960	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9347760	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9364688	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9364691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9364692	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1019551	chr6:163842358-163965216	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1017495	chr6:163856399-163981095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv524205	chr6:163919517-163938331	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2763608	chr6:163920117-163943429	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9364689	SESTD1	trans	cerebellum	SCAN
rs9364689	QKI	Cis_1M	lymphoblastoid	RTeQTL
rs9364689	LOC285796	cis	lymphoblastoid	seeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163911800-163934800	Weak transcription	Pancreas	Pancrea
2	chr6:163920200-163934800	Weak transcription	Ovary	ovary
3	chr6:163923800-163929800	Enhancers	Brain Hippocampus Middle	brain
4	chr6:163924400-163931600	Weak transcription	Aorta	Aorta
5	chr6:163925000-163929400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
6	chr6:163925400-163931000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:163925600-163929400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:163925600-163929600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr6:163925600-163929600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
10	chr6:163925600-163930600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:163925800-163929600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
12	chr6:163926000-163929400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:163926000-163930600	ZNF genes & repeats	Fetal Muscle Leg	muscle
14	chr6:163926600-163934800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:163926600-163934800	Weak transcription	Lung	lung
16	chr6:163926600-163934800	Weak transcription	Psoas Muscle	Psoas
17	chr6:163926600-163934800	Weak transcription	Right Atrium	heart
18	chr6:163926600-163946200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:163926600-163946600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:163926600-163991800	Weak transcription	Esophagus	oesophagus
21	chr6:163926800-163930200	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:163926800-163931400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr6:163926800-163934800	Weak transcription	Right Ventricle	heart
24	chr6:163927200-163931000	Weak transcription	Left Ventricle	heart
25	chr6:163927200-163951600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:163927400-163929600	ZNF genes & repeats	Fetal Lung	lung
27	chr6:163927400-163929600	ZNF genes & repeats	K562	blood
28	chr6:163927800-163929400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr6:163927800-163929600	ZNF genes & repeats	HepG2	liver
30	chr6:163927800-163929800	ZNF genes & repeats	Primary B cells from cord blood	blood
31	chr6:163928000-163929600	ZNF genes & repeats	Liver	Liver
32	chr6:163928000-163930400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:163928000-163930600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
34	chr6:163928200-163951600	Weak transcription	Spleen	Spleen
35	chr6:163928400-163931800	Weak transcription	NH-A	brain
36	chr6:163928600-163931000	Enhancers	Brain Substantia Nigra	brain
37	chr6:163928600-163931200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:163928600-163934000	Weak transcription	Fetal Heart	heart
39	chr6:163928600-163938400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:163928600-163941000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr6:163928800-163930400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:163928800-163934800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr6:163928800-163942800	Weak transcription	HSMM	muscle
44	chr6:163928800-163944000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr6:163928800-163946600	Weak transcription	HUVEC	blood vessel
46	chr6:163929000-163930200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:163929000-163930400	Weak transcription	Osteobl	bone
48	chr6:163929000-163933200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:163929000-163938000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:163929000-163947200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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