Variant report

Variant	rs608248
Chromosome Location	chr11:66562248-66562249
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12577111	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap]
rs12805133	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1791684	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs2276138	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs2513658	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3741363	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs4930387	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4930391	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs498045	0.82[CHB][hapmap]
rs503250	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs508443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs535211	0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs543191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551708	0.89[TSI][hapmap]
rs556759	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs569818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577023	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs580910	0.83[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap]
rs594313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs627330	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs682842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7107944	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv427891	chr11:66456140-66606701	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv468602	chr11:66468469-66634397	Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv555225	chr11:66468469-66634397	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	nsv516087	chr11:66516049-66579572	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv508638	chr11:66541653-66643634	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs608248	LRFN4	cis	multi-tissue	Pritchard
rs608248	ACTN3	cis	lymphoblastoid	seeQTL
rs608248	ESRRA	cis	cerebellum	SCAN
rs608248	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs608248	SYT12	cis	parietal	SCAN
rs608248	CCS	cis	multi-tissue	Pritchard
rs608248	ACTN3	cis	Muscle Skeletal	GTEx
rs608248	CCS	cis	lymphoblastoid	seeQTL
rs608248	EHBP1L1	cis	cerebellum	SCAN
rs608248	MACROD1	cis	parietal	SCAN
rs608248	SLC25A45	cis	parietal	SCAN
rs608248	CTSF	cis	multi-tissue	Pritchard

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66513400-66606800	Weak transcription	Brain Angular Gyrus	brain
2	chr11:66527000-66574200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr11:66527000-66595600	Weak transcription	HSMM	muscle
4	chr11:66527400-66571600	Weak transcription	Primary T cells from cord blood	blood
5	chr11:66530000-66571400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr11:66530000-66605400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr11:66530200-66582400	Weak transcription	HUVEC	blood vessel
8	chr11:66530600-66575200	Weak transcription	Esophagus	oesophagus
9	chr11:66530600-66600000	Weak transcription	Fetal Muscle Leg	muscle
10	chr11:66530800-66581800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:66531000-66572800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr11:66531200-66577800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:66531400-66578000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:66531800-66569400	Weak transcription	Brain Germinal Matrix	brain
15	chr11:66532000-66568400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:66536600-66572000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:66538200-66575800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:66539800-66571400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:66544000-66609600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:66548400-66571400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr11:66550400-66571400	Weak transcription	Fetal Brain Female	brain
22	chr11:66554600-66605800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr11:66554800-66568000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr11:66556200-66577600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr11:66556200-66577600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr11:66556200-66603000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:66556600-66571200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:66556600-66583600	Weak transcription	Fetal Stomach	stomach
29	chr11:66556600-66586000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr11:66556800-66568000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:66556800-66589200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr11:66556800-66607400	Weak transcription	Fetal Lung	lung
33	chr11:66557000-66572400	Weak transcription	Thymus	Thymus
34	chr11:66557200-66567800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:66557200-66569800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:66557200-66571000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:66557200-66582400	Weak transcription	NHEK	skin
38	chr11:66557400-66568200	Weak transcription	Fetal Thymus	thymus
39	chr11:66557400-66575600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr11:66558000-66583000	Weak transcription	Hela-S3	cervix
41	chr11:66558200-66572800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr11:66558600-66572800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr11:66558800-66568400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:66560400-66564800	Weak transcription	GM12878-XiMat	blood
45	chr11:66560400-66569000	Weak transcription	Fetal Intestine Small	intestine
46	chr11:66560400-66575000	Weak transcription	Fetal Intestine Large	intestine
47	chr11:66560400-66595600	Weak transcription	A549	lung
48	chr11:66560400-66605400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr11:66560800-66564000	Weak transcription	Primary B cells from cord blood	blood
50	chr11:66561600-66609400	Weak transcription	Colonic Mucosa	Colon

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