Variant report

Variant	rs9405829
Chromosome Location	chr6:5369738-5369739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5364063..5366771-chr6:5369592..5371297,2	K562	blood:
2	chr6:5364063..5367061-chr6:5369428..5371092,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs2024998	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2552300	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2552301	0.86[JPT][hapmap]
rs2753253	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2753254	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs3763182	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55716067	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61315229	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62386863	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62386900	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs708036	0.86[JPT][hapmap]
rs72815645	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7774214	0.86[JPT][hapmap]
rs797131	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs809962	0.86[JPT][hapmap]
rs9378421	0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9378422	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9378946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9392079	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9392672	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9392676	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9392678	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9392679	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9405819	0.86[JPT][hapmap]
rs9405820	0.86[JPT][hapmap]
rs9405821	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9405824	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9405828	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
4	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1029609	chr6:5187633-5397254	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1035080	chr6:5206533-5396019	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv538116	chr6:5206533-5396019	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv830578	chr6:5264086-5455570	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1022738	chr6:5298362-5411645	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv600883	chr6:5302619-5400658	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv883417	chr6:5307432-5431340	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv883418	chr6:5307432-5501389	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv1015643	chr6:5311590-5452427	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv1034607	chr6:5311590-5573514	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv538120	chr6:5311590-5573514	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv883419	chr6:5316399-5400658	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv1030744	chr6:5328012-5458222	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv600884	chr6:5338955-5394992	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9405829	NQO2	cis	cerebellum	SCAN
rs9405829	BMP6	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5326600-5385000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:5334800-5371000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:5337800-5380800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr6:5354600-5379600	Weak transcription	GM12878-XiMat	blood
5	chr6:5360200-5371000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:5362000-5370800	Weak transcription	Colonic Mucosa	Colon
7	chr6:5362200-5371200	Weak transcription	Brain Substantia Nigra	brain
8	chr6:5362200-5372000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:5362400-5375200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:5362400-5384600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:5362600-5370000	Weak transcription	Brain Germinal Matrix	brain
12	chr6:5366400-5372200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:5366600-5375400	Weak transcription	Brain Angular Gyrus	brain
14	chr6:5367000-5378600	Weak transcription	K562	blood
15	chr6:5367200-5386000	Weak transcription	Fetal Brain Female	brain
16	chr6:5367400-5371600	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:5367400-5372400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr6:5367400-5379800	Weak transcription	HSMMtube	muscle
19	chr6:5367800-5370200	Weak transcription	HSMM	muscle
20	chr6:5367800-5371000	Weak transcription	Brain Anterior Caudate	brain
21	chr6:5367800-5371200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:5368000-5375000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:5368000-5378400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:5368400-5398600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:5368600-5369800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:5368600-5370000	Strong transcription	Dnd41	blood
27	chr6:5368600-5370200	Strong transcription	HepG2	liver
28	chr6:5368600-5370400	Strong transcription	Primary B cells from peripheral blood	blood
29	chr6:5368600-5370600	Strong transcription	Stomach Smooth Muscle	stomach
30	chr6:5368600-5371400	Strong transcription	Primary T cells from cord blood	blood
31	chr6:5368600-5371400	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr6:5368600-5374400	Strong transcription	Primary B cells from cord blood	blood
33	chr6:5368800-5369800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:5368800-5369800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:5368800-5369800	Strong transcription	Placenta	Placenta
36	chr6:5368800-5370000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr6:5368800-5370000	Strong transcription	Duodenum Mucosa	Duodenum
38	chr6:5368800-5370000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:5368800-5370000	Strong transcription	Gastric	stomach
40	chr6:5368800-5370000	Strong transcription	Right Ventricle	heart
41	chr6:5368800-5370400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr6:5368800-5370600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr6:5368800-5370600	Strong transcription	Adipose Nuclei	Adipose
44	chr6:5368800-5370600	Strong transcription	Brain Hippocampus Middle	brain
45	chr6:5368800-5371400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr6:5368800-5371400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:5368800-5378400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:5369000-5369800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr6:5369000-5369800	Strong transcription	Fetal Intestine Large	intestine
50	chr6:5369000-5370000	Strong transcription	Thymus	Thymus

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