Variant report

Variant	rs12548006
Chromosome Location	chr8:38912667-38912668
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10089487	0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs10113077	1.00[JPT][hapmap]
rs10958813	0.87[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11777149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777376	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11787126	0.91[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12056655	0.86[ASW][hapmap];0.87[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12541231	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];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12543388	0.82[EUR][1000 genomes]
rs12543921	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12546318	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12548416	0.82[EUR][1000 genomes]
rs12548948	0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12549547	0.91[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13248324	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13256952	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]
rs13268394	0.86[ASW][hapmap];0.87[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13274567	0.91[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34070223	0.82[EUR][1000 genomes]
rs34138150	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34185462	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35391544	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35534138	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4129095	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];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4495395	0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs4543512	0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4733897	0.88[JPT][hapmap]
rs4733901	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4733905	0.86[ASW][hapmap];0.91[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4733959	0.82[JPT][hapmap]
rs4733964	0.88[JPT][hapmap]
rs4733970	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6474516	0.88[JPT][hapmap]
rs66925354	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7832578	0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs7838874	0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs9643858	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9643902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9643904	0.91[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9643906	0.91[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:38882000-38913600	Weak transcription	Fetal Kidney	kidney
2	chr8:38883000-38913000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr8:38890200-38914400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr8:38890400-38919800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr8:38896000-38918400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr8:38896000-38925000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr8:38896200-38916000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr8:38896400-38916400	Weak transcription	K562	blood
9	chr8:38896600-38912800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr8:38897400-38963400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr8:38897600-38918600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr8:38899800-38916600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr8:38900600-38912800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr8:38900600-38918400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr8:38900600-38925600	Weak transcription	Small Intestine	intestine
16	chr8:38902400-38916400	Weak transcription	Right Ventricle	heart
17	chr8:38902400-38920000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr8:38902400-38947600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr8:38903000-38921400	Weak transcription	Fetal Heart	heart
20	chr8:38904600-38913200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr8:38904600-38915200	Weak transcription	Lung	lung
22	chr8:38905000-38913800	Weak transcription	Fetal Brain Male	brain
23	chr8:38905000-38960000	Weak transcription	HSMMtube	muscle
24	chr8:38906000-38912800	Weak transcription	Primary B cells from cord blood	blood
25	chr8:38906000-38922600	Strong transcription	HSMM	muscle
26	chr8:38906800-38915000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr8:38906800-38921400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr8:38907600-38916600	Strong transcription	NH-A	brain
29	chr8:38908200-38918400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr8:38908400-38915000	Strong transcription	HUVEC	blood vessel
31	chr8:38908800-38915000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr8:38908800-38916200	Weak transcription	Fetal Brain Female	brain
33	chr8:38909000-38922800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr8:38909200-38913800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr8:38910200-38915800	Strong transcription	HepG2	liver
36	chr8:38910200-38922800	Strong transcription	A549	lung
37	chr8:38910400-38912800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr8:38910600-38916600	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr8:38910800-38920800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr8:38911000-38923600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr8:38911200-38912800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr8:38911200-38916400	Strong transcription	NHLF	lung
43	chr8:38911200-38918600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr8:38911200-38918800	Strong transcription	NHEK	skin
45	chr8:38911200-38921000	Strong transcription	Placenta	Placenta
46	chr8:38911200-38921200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr8:38911200-38922600	Strong transcription	Dnd41	blood
48	chr8:38911200-38923400	Strong transcription	Osteobl	bone
49	chr8:38911400-38913000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr8:38911400-38914800	Strong transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links