Variant report

Variant	rs13256952
Chromosome Location	chr8:38921296-38921297
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	chr8:38920268..38922257-chr8:38925771..38928354,3	K562	blood:
2	chr8:38915849..38919016-chr8:38921261..38923485,4	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10089487	0.86[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs10113077	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs10958813	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11777149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11777376	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11787126	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]
rs11985898	0.81[MEX][hapmap]
rs12056655	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12541231	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12543388	0.83[EUR][1000 genomes]
rs12543921	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12546318	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12548006	0.86[ASW][hapmap];0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12548416	0.83[EUR][1000 genomes]
rs12548948	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12549232	0.90[MEX][hapmap];0.82[TSI][hapmap]
rs12549547	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]
rs13248324	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13268394	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13274567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34070223	0.83[EUR][1000 genomes]
rs34138150	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34185462	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35391544	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35534138	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4129095	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4236757	0.82[TSI][hapmap]
rs4495395	0.81[CHB][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs4543512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4733897	0.81[JPT][hapmap]
rs4733901	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4733905	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4733964	0.81[JPT][hapmap]
rs4733970	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6474516	0.81[JPT][hapmap]
rs66925354	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7832578	0.81[CHB][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs7838874	0.81[CHB][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap]
rs9643858	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9643902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9643904	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9643906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3445313	chr8:38886844-38936643	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
2	esv3325011	chr8:38899844-38936643	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13256952	ADAM32	cis	cerebellum	SCAN
rs13256952	TM2D2	cis	cerebellum	SCAN
rs13256952	PLEKHA2	cis	lymphoblastoid	seeQTL
rs13256952	SGK196	cis	parietal	SCAN
rs13256952	TM2D2	cis	parietal	SCAN
rs13256952	DDHD2	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:38896000-38925000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr8:38897400-38963400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:38900600-38925600	Weak transcription	Small Intestine	intestine
4	chr8:38902400-38947600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr8:38903000-38921400	Weak transcription	Fetal Heart	heart
6	chr8:38905000-38960000	Weak transcription	HSMMtube	muscle
7	chr8:38906000-38922600	Strong transcription	HSMM	muscle
8	chr8:38906800-38921400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr8:38909000-38922800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr8:38910200-38922800	Strong transcription	A549	lung
11	chr8:38911000-38923600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr8:38911200-38922600	Strong transcription	Dnd41	blood
13	chr8:38911200-38923400	Strong transcription	Osteobl	bone
14	chr8:38911400-38922000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:38911400-38923600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr8:38911600-38930000	Weak transcription	Pancreas	Pancrea
17	chr8:38911600-38933200	Weak transcription	Colon Smooth Muscle	Colon
18	chr8:38911600-38947800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr8:38911800-38923000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr8:38911800-38923600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr8:38911800-38923600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr8:38911800-38949000	Weak transcription	Brain Substantia Nigra	brain
23	chr8:38911800-38964800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr8:38912000-38949000	Weak transcription	Brain Angular Gyrus	brain
25	chr8:38912400-38922600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr8:38912800-38923600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr8:38912800-38923600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr8:38913200-38922800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr8:38913400-38923600	Strong transcription	Fetal Lung	lung
30	chr8:38913800-38921600	Strong transcription	Fetal Muscle Leg	muscle
31	chr8:38913800-38921800	Strong transcription	Fetal Intestine Large	intestine
32	chr8:38913800-38922600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr8:38914000-38929400	Weak transcription	Liver	Liver
34	chr8:38914200-38934000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr8:38914400-38964800	Weak transcription	Fetal Kidney	kidney
36	chr8:38914600-38935000	Weak transcription	Brain Anterior Caudate	brain
37	chr8:38914800-38964800	Weak transcription	Colonic Mucosa	Colon
38	chr8:38915000-38922600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr8:38915200-38940000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr8:38915400-38922600	Strong transcription	GM12878-XiMat	blood
41	chr8:38916000-38921600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr8:38916000-38921600	Strong transcription	Fetal Stomach	stomach
43	chr8:38916200-38921800	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr8:38916600-38922600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr8:38916600-38923600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr8:38917000-38922400	Strong transcription	HUVEC	blood vessel
47	chr8:38917200-38923200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr8:38917400-38921600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr8:38917400-38922800	Strong transcription	NH-A	brain
50	chr8:38917400-38923000	Strong transcription	Muscle Satellite Cultured Cells	--

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