Variant report

Variant	rs9480548
Chromosome Location	chr6:151024867-151024868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10872666	0.93[JPT][hapmap]
rs12664155	1.00[CEU][hapmap]
rs1466725	0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs17080212	1.00[CEU][hapmap]
rs17080238	1.00[CEU][hapmap]
rs1968999	0.85[EUR][1000 genomes]
rs2279628	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs3734411	1.00[CEU][hapmap]
rs4869689	0.85[CEU][hapmap]
rs4869932	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs4869934	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869936	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869938	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869939	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5029652	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902743	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748886	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs7772795	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs9478784	0.82[AMR][1000 genomes]
rs9478785	0.82[AFR][1000 genomes]
rs9478786	1.00[EUR][1000 genomes]
rs9478790	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9478791	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs9480534	0.85[EUR][1000 genomes]
rs9480535	0.85[EUR][1000 genomes]
rs9480536	0.85[EUR][1000 genomes]
rs9480537	0.80[AFR][1000 genomes]
rs9480538	0.83[AFR][1000 genomes]
rs9480540	1.00[EUR][1000 genomes]
rs9480543	0.92[AFR][1000 genomes]
rs9480545	0.92[AFR][1000 genomes]
rs9480549	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480551	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];0.85[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986516	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986520	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986597	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1030326	chr6:150967665-151641372	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv966635	chr6:151018787-151025050	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:151015200-151033200	Weak transcription	Right Atrium	heart
2	chr6:151015400-151025600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:151017600-151029200	Weak transcription	Lung	lung
4	chr6:151017800-151025200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:151017800-151025600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:151017800-151027200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:151018800-151028600	Weak transcription	Adipose Nuclei	Adipose
8	chr6:151019000-151033000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:151019000-151033200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:151019000-151035200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:151020800-151025600	Weak transcription	Esophagus	oesophagus
12	chr6:151021400-151025400	Enhancers	Primary B cells from cord blood	blood
13	chr6:151021400-151026400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr6:151021400-151029000	Weak transcription	Left Ventricle	heart
15	chr6:151021600-151025600	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:151021600-151026800	Enhancers	Primary B cells from peripheral blood	blood
17	chr6:151021600-151033000	Weak transcription	Fetal Stomach	stomach
18	chr6:151021600-151040600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:151022000-151025200	Weak transcription	Spleen	Spleen
20	chr6:151023400-151025400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr6:151023600-151025400	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr6:151023800-151025200	Enhancers	Fetal Thymus	thymus
23	chr6:151024000-151025400	Weak transcription	Thymus	Thymus
24	chr6:151024000-151027600	Enhancers	Placenta	Placenta
25	chr6:151024200-151026600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:151024200-151028600	Weak transcription	Small Intestine	intestine
27	chr6:151024200-151034200	Weak transcription	Right Ventricle	heart
28	chr6:151024400-151028800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:151024400-151032800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:151024800-151027000	Enhancers	Placenta Amnion	Placenta Amnion

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