Variant report

Variant	rs13259875
Chromosome Location	chr8:19495598-19495599
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10101438	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10282953	1.00[JPT][hapmap]
rs10283283	1.00[JPT][hapmap]
rs13252345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17128770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17480734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs28483049	0.80[ASN][1000 genomes]
rs2957616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2975424	1.00[JPT][hapmap]
rs4273864	1.00[JPT][hapmap]
rs4922074	1.00[JPT][hapmap]
rs7001715	1.00[JPT][hapmap]
rs7003476	1.00[JPT][hapmap]
rs7017890	1.00[JPT][hapmap]
rs867930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv1015448	chr8:19474715-19520367	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13259875	ChGn	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19482000-19520000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr8:19483200-19495600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr8:19483200-19495600	Weak transcription	Right Atrium	heart
4	chr8:19485400-19499200	Weak transcription	Placenta	Placenta
5	chr8:19485400-19500000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr8:19488800-19501200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr8:19489000-19497800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr8:19489800-19500000	Weak transcription	Lung	lung
9	chr8:19490800-19495600	Weak transcription	Gastric	stomach
10	chr8:19490800-19497200	Weak transcription	Hela-S3	cervix
11	chr8:19491000-19495800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr8:19491200-19495800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr8:19491400-19499200	Weak transcription	Fetal Lung	lung
14	chr8:19493000-19495600	Weak transcription	Right Ventricle	heart
15	chr8:19493000-19495600	Weak transcription	Spleen	Spleen
16	chr8:19493200-19495600	Weak transcription	Brain Hippocampus Middle	brain
17	chr8:19493400-19497000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr8:19494200-19497600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr8:19494800-19496000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr8:19495000-19495600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
21	chr8:19495000-19495600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr8:19495000-19495800	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr8:19495000-19495800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr8:19495000-19496000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
25	chr8:19495000-19496000	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr8:19495000-19496000	Flanking Active TSS	GM12878-XiMat	blood
27	chr8:19495000-19496400	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr8:19495000-19497600	Genic enhancers	A549	lung
29	chr8:19495000-19498600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
30	chr8:19495200-19495600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr8:19495200-19495600	Flanking Active TSS	Primary B cells from peripheral blood	blood
32	chr8:19495200-19495600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr8:19495200-19495600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr8:19495200-19495800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr8:19495200-19495800	Enhancers	Primary T cells from cord blood	blood
36	chr8:19495200-19496000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr8:19495200-19497400	Enhancers	Brain Cingulate Gyrus	brain
38	chr8:19495200-19497600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr8:19495200-19497800	Enhancers	Brain Substantia Nigra	brain
40	chr8:19495200-19498000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
41	chr8:19495200-19498400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
42	chr8:19495400-19496000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
43	chr8:19495400-19496000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr8:19495400-19496000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr8:19495400-19496000	Enhancers	Left Ventricle	heart
46	chr8:19495400-19496000	Enhancers	Pancreas	Pancrea
47	chr8:19495400-19496400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
48	chr8:19495400-19497600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links