Variant report

Variant	rs828605
Chromosome Location	chr3:98495828-98495829
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98494773..98497684-chr3:98500222..98503484,3	K562	blood:

Variant related genes	Relation type
ENSG00000064225	Chromatin interaction
ENSG00000249274	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10935514	1.00[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs1095911	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12632798	0.96[CEU][hapmap];0.89[JPT][hapmap]
rs12636683	0.91[EUR][1000 genomes]
rs13071075	0.87[EUR][1000 genomes]
rs13316760	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs1371687	1.00[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs2439237	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs278376	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs278379	0.92[CEU][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs278380	1.00[CEU][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs278381	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs278382	0.96[CEU][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs278387	1.00[ASW][hapmap];0.87[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs278388	1.00[CEU][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs278390	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4857415	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6767370	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6791389	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7615856	0.92[CEU][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs828603	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs828610	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs828614	0.92[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs828616	0.82[ASW][hapmap];0.92[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs828617	0.92[CEU][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs828618	0.84[CEU][hapmap]
rs828621	0.91[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs852701	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8833	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs955351	0.88[CEU][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs828605	ZBTB11	cis	cerebellum	SCAN
rs828605	DCBLD2	cis	Adipose Subcutaneous	GTEx
rs828605	ST3GAL6	cis	multi-tissue	Pritchard

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:98482400-98496000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:98482600-98501800	Weak transcription	Fetal Stomach	stomach
4	chr3:98482800-98497400	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:98483000-98497400	Weak transcription	Spleen	Spleen
6	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
9	chr3:98483800-98496400	Weak transcription	Fetal Lung	lung
10	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:98484000-98498000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
15	chr3:98485000-98496200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:98488200-98496800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:98488600-98496200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:98488600-98497200	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:98488600-98497200	Weak transcription	Fetal Kidney	kidney
20	chr3:98489600-98497000	Weak transcription	Lung	lung
21	chr3:98489800-98496000	Weak transcription	Stomach Mucosa	stomach
22	chr3:98489800-98496200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:98489800-98496400	Weak transcription	Placenta	Placenta
24	chr3:98489800-98496600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:98489800-98496600	Weak transcription	Adipose Nuclei	Adipose
26	chr3:98489800-98497000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:98489800-98497400	Weak transcription	Right Ventricle	heart
28	chr3:98489800-98497600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:98489800-98503000	Weak transcription	Psoas Muscle	Psoas
30	chr3:98490000-98496200	Weak transcription	Brain Substantia Nigra	brain
31	chr3:98490000-98496400	Weak transcription	Brain Anterior Caudate	brain
32	chr3:98490200-98496000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:98490200-98496000	Weak transcription	Brain Angular Gyrus	brain
34	chr3:98490200-98496400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:98490400-98497400	Weak transcription	Fetal Brain Female	brain
37	chr3:98491600-98496600	Strong transcription	Primary hematopoietic stem cells	blood
38	chr3:98491600-98497400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:98493600-98496800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:98493800-98496000	Weak transcription	NH-A	brain
42	chr3:98493800-98498400	Enhancers	HepG2	liver
43	chr3:98493800-98499600	Enhancers	Fetal Intestine Large	intestine
44	chr3:98494000-98497000	Strong transcription	Thymus	Thymus
45	chr3:98494400-98497200	Genic enhancers	Monocytes-CD14+_RO01746	blood
46	chr3:98494400-98498400	Enhancers	Fetal Intestine Small	intestine
47	chr3:98494600-98497600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:98494600-98499200	Genic enhancers	Primary monocytes fromperipheralblood	blood
49	chr3:98494600-98506000	Enhancers	Aorta	Aorta
50	chr3:98494800-98496000	Weak transcription	Fetal Heart	heart

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