Variant report

Variant	rs4244454
Chromosome Location	chr8:19456473-19456474
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1013438	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10888166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204046	0.93[CEU][hapmap];0.83[TSI][hapmap]
rs11204057	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2958576	0.93[CEU][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4410924	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs4433157	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4483172	0.81[CEU][hapmap]
rs4618713	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4633073	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4922041	0.81[CEU][hapmap]
rs4922045	0.81[CEU][hapmap]
rs4922046	0.80[CEU][hapmap]
rs4922047	0.81[CEU][hapmap]
rs4922065	0.93[CEU][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4922066	0.83[CEU][hapmap]
rs59047686	1.00[ASN][1000 genomes]
rs59296505	1.00[ASN][1000 genomes]
rs6586843	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6586844	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6586849	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6998334	0.81[CEU][hapmap]
rs7016845	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7017776	0.81[CEU][hapmap]
rs73214643	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73214644	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7831489	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7838412	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7841402	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533109	chr8:18845845-19456780	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
3	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv34007	chr8:19252602-19482098	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv890626	chr8:19383697-19483259	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv890627	chr8:19389865-19561997	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv610754	chr8:19419494-19525294	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1021575	chr8:19430653-19623452	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv465601	chr8:19434021-19456473	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv610755	chr8:19434021-19456473	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv610756	chr8:19434021-19471977	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1025271	chr8:19435147-19574969	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4244454	PDGFRL	cis	cerebellum	SCAN
rs4244454	CSGALNACT1	cis	cerebellum	SCAN
rs4244454	CSGALNACT1	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19434000-19457800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr8:19435000-19457200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr8:19437800-19459600	Weak transcription	Right Ventricle	heart
4	chr8:19439000-19458600	Weak transcription	Brain Anterior Caudate	brain
5	chr8:19445000-19457600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr8:19445600-19457200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr8:19445600-19457200	Weak transcription	Left Ventricle	heart
8	chr8:19445600-19459600	Weak transcription	Placenta	Placenta
9	chr8:19445600-19461400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr8:19445600-19481400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr8:19448000-19459800	Weak transcription	Gastric	stomach
12	chr8:19451000-19459800	Weak transcription	Lung	lung
13	chr8:19451600-19457400	Weak transcription	Right Atrium	heart
14	chr8:19451800-19459200	Weak transcription	NHLF	lung
15	chr8:19452800-19457600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr8:19453600-19459800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:19453800-19458600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr8:19454000-19457200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr8:19454000-19458000	Genic enhancers	A549	lung
20	chr8:19454000-19458400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr8:19454200-19460800	Weak transcription	Hela-S3	cervix
22	chr8:19455000-19457600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr8:19455200-19456800	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr8:19455400-19456600	Strong transcription	Primary T cells from cord blood	blood
25	chr8:19455600-19456600	Enhancers	Fetal Lung	lung
26	chr8:19455600-19457400	Weak transcription	Aorta	Aorta
27	chr8:19455600-19459200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr8:19455800-19457200	Weak transcription	Primary B cells from cord blood	blood
29	chr8:19455800-19457200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr8:19455800-19459800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr8:19456000-19457200	Weak transcription	Ovary	ovary
32	chr8:19456200-19456600	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr8:19456200-19456800	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr8:19456200-19479600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr8:19456400-19456600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr8:19456400-19456600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr8:19456400-19456600	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr8:19456400-19456600	Enhancers	Spleen	Spleen
39	chr8:19456400-19456800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
40	chr8:19456400-19457200	Enhancers	Brain Angular Gyrus	brain
41	chr8:19456400-19457400	Enhancers	Esophagus	oesophagus

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