Variant report

Variant	rs9481048
Chromosome Location	chr6:110555467-110555468
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11153226	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11751590	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11757055	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12110744	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12660791	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1462492	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1462493	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17071325	0.88[AMR][1000 genomes]
rs17071330	0.88[AMR][1000 genomes]
rs17071358	0.81[AMR][1000 genomes]
rs2334319	0.85[CEU][hapmap]
rs2334322	0.90[AMR][1000 genomes]
rs41288582	0.86[AMR][1000 genomes]
rs4257894	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4299857	1.00[JPT][hapmap]
rs4339500	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4509164	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4945850	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4945851	0.86[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs4947048	0.82[ASN][1000 genomes]
rs4947051	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4947058	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4947060	0.86[AMR][1000 genomes]
rs55649499	0.88[AMR][1000 genomes]
rs56122480	0.81[ASN][1000 genomes]
rs56287427	0.82[ASN][1000 genomes]
rs57983455	0.86[ASN][1000 genomes]
rs6568633	0.82[ASN][1000 genomes]
rs6568634	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6909242	0.83[AMR][1000 genomes]
rs6913554	0.93[CHB][hapmap];0.85[ASN][1000 genomes]
rs6918148	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs6926540	0.84[ASN][1000 genomes]
rs6927667	0.82[ASN][1000 genomes]
rs6927697	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6927722	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6938106	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6938139	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6938653	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs73535817	0.81[ASN][1000 genomes]
rs73535821	0.81[ASN][1000 genomes]
rs73535837	0.82[ASN][1000 genomes]
rs73535838	0.82[ASN][1000 genomes]
rs73537927	0.84[ASN][1000 genomes]
rs73537938	0.86[ASN][1000 genomes]
rs73537949	0.87[ASN][1000 genomes]
rs7744828	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7746681	0.90[AMR][1000 genomes]
rs7749663	0.86[AMR][1000 genomes]
rs7766757	0.90[AMR][1000 genomes]
rs7766850	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9481045	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9481047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9481050	0.83[AMR][1000 genomes]
rs9487317	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9487318	0.95[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9487319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9487321	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487325	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs9487327	0.81[AMR][1000 genomes]
rs9487331	0.83[AMR][1000 genomes]
rs9487333	0.90[AMR][1000 genomes]
rs9487334	0.84[AMR][1000 genomes]
rs9487337	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1792799	chr6:110411065-110566597	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' 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
2	nsv948824	chr6:110443685-110889332	Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	esv1801843	chr6:110506109-110566328	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv949643	chr6:110537685-110889332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers 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	nsv965659	chr6:110555126-110561922	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9481048	FIG4	cis	parietal	SCAN
rs9481048	WASF1	cis	Muscle Skeletal	GTEx
rs9481048	WASF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110528200-110557400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:110530000-110556400	Weak transcription	Small Intestine	intestine
3	chr6:110530800-110558400	Weak transcription	Stomach Mucosa	stomach
4	chr6:110537800-110558600	Weak transcription	Gastric	stomach
5	chr6:110539000-110563600	Weak transcription	Lung	lung
6	chr6:110539000-110580200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:110539200-110558200	Weak transcription	Brain Substantia Nigra	brain
8	chr6:110539200-110560000	Weak transcription	Esophagus	oesophagus
9	chr6:110539400-110558400	Weak transcription	Fetal Brain Male	brain
10	chr6:110539400-110558600	Weak transcription	HUVEC	blood vessel
11	chr6:110540000-110567000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:110541200-110567200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:110544200-110556800	Weak transcription	HMEC	breast
14	chr6:110544600-110566400	Weak transcription	Fetal Stomach	stomach
15	chr6:110547000-110576600	Weak transcription	Pancreas	Pancrea
16	chr6:110548200-110556200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:110548800-110558600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:110549000-110562400	Weak transcription	Psoas Muscle	Psoas
19	chr6:110549000-110567400	Weak transcription	Fetal Intestine Large	intestine
20	chr6:110549200-110559000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:110549400-110557000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:110549400-110557000	Weak transcription	Fetal Lung	lung
23	chr6:110549400-110558400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:110549400-110560800	Weak transcription	K562	blood
25	chr6:110549400-110561000	Weak transcription	NH-A	brain
26	chr6:110549400-110561800	Weak transcription	Fetal Brain Female	brain
27	chr6:110549400-110562200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:110549400-110580400	Weak transcription	Brain Angular Gyrus	brain
29	chr6:110549600-110559000	Weak transcription	Thymus	Thymus
30	chr6:110549600-110560000	Weak transcription	Fetal Muscle Leg	muscle
31	chr6:110549600-110562000	Weak transcription	Brain Germinal Matrix	brain
32	chr6:110549600-110568600	Weak transcription	Left Ventricle	heart
33	chr6:110550600-110608200	Weak transcription	Fetal Kidney	kidney
34	chr6:110550800-110557000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:110550800-110566400	Weak transcription	Ovary	ovary
36	chr6:110550800-110567200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:110551000-110559600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:110551200-110560200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:110551400-110555600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr6:110551400-110556600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:110551400-110556800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:110551400-110557000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:110551400-110558400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:110551400-110558600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:110551400-110559000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:110551400-110559800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:110551400-110560000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:110551400-110560000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr6:110551400-110560000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr6:110551400-110560000	Weak transcription	Rectal Mucosa Donor 31	rectum

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