Variant report

Variant	rs4299828
Chromosome Location	chr6:38177667-38177668
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1931765	0.94[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1931766	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2050161	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2395695	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2395696	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4711527	0.94[CEU][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs4714128	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4714129	0.94[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4714130	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4714131	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4714132	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4714133	0.85[EUR][1000 genomes]
rs6458045	0.94[CEU][hapmap]
rs6458047	0.94[CEU][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6904507	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6915783	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6917654	0.94[CEU][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6924088	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6930118	0.93[EUR][1000 genomes]
rs6935617	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7738411	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9380722	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9380724	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9470833	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv522522	chr6:38131442-38207636	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv885819	chr6:38148770-38190439	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv520053	chr6:38154941-38207636	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv3438946	chr6:38177563-38177935	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4299828	ZFAND3	cis	cerebellum	SCAN
rs4299828	TREML4	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38147400-38180400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:38160600-38179600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:38160800-38201400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr6:38162000-38179800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:38162600-38180000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:38166800-38194800	Weak transcription	Primary B cells from cord blood	blood
7	chr6:38167000-38210400	Weak transcription	Primary T cells from cord blood	blood
8	chr6:38174200-38180200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:38175400-38179600	Weak transcription	Psoas Muscle	Psoas
10	chr6:38175400-38180000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:38175800-38178800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:38176000-38179600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:38176000-38184800	Enhancers	Fetal Muscle Leg	muscle
14	chr6:38176200-38177800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:38176200-38178200	Weak transcription	Fetal Kidney	kidney
16	chr6:38176200-38181400	Enhancers	Fetal Stomach	stomach
17	chr6:38176800-38177800	Enhancers	Primary hematopoietic stem cells	blood
18	chr6:38176800-38177800	Enhancers	Fetal Muscle Trunk	muscle
19	chr6:38176800-38178000	Enhancers	Fetal Thymus	thymus
20	chr6:38176800-38178800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:38176800-38179800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:38177000-38177800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:38177000-38177800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:38177000-38178000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr6:38177000-38178000	Enhancers	Primary T cells fromperipheralblood	blood
26	chr6:38177000-38178400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr6:38177000-38178600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr6:38177000-38178800	Enhancers	Fetal Lung	lung
29	chr6:38177200-38177800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:38177200-38177800	Enhancers	Aorta	Aorta
31	chr6:38177200-38178000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr6:38177200-38178000	Enhancers	Fetal Brain Male	brain
33	chr6:38177200-38178200	Weak transcription	Brain Angular Gyrus	brain
34	chr6:38177200-38178400	Enhancers	Lung	lung
35	chr6:38177200-38178400	Enhancers	Small Intestine	intestine
36	chr6:38177200-38178600	Enhancers	Brain Hippocampus Middle	brain
37	chr6:38177200-38178800	Enhancers	Ovary	ovary
38	chr6:38177200-38179000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:38177200-38179800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:38177400-38177800	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr6:38177400-38177800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:38177400-38177800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:38177400-38177800	Enhancers	Rectal Smooth Muscle	rectum
44	chr6:38177400-38177800	Enhancers	Spleen	Spleen
45	chr6:38177400-38178000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:38177400-38178000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr6:38177400-38178200	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr6:38177400-38178800	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr6:38177400-38178800	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr6:38177400-38179000	Enhancers	Brain Cingulate Gyrus	brain

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