Variant report

Variant	rs682842
Chromosome Location	chr11:66568943-66568944
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	chr11:66568727..66571810-chr11:66574356..66577188,3	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12577111	0.83[ASW][hapmap];0.82[MKK][hapmap]
rs2513658	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[LWK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4930391	0.92[ASW][hapmap];1.00[CEU][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs508443	1.00[CEU][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs543191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs551708	0.89[TSI][hapmap]
rs566673	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs569818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs580910	0.83[ASW][hapmap];0.82[MKK][hapmap]
rs594313	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs608248	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]
rs627330	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7107944	0.83[AMR][1000 genomes];0.97[EUR][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs682842	CCS	cis	lymphoblastoid	seeQTL
rs682842	SLC25A45	cis	parietal	SCAN
rs682842	EHBP1L1	cis	cerebellum	SCAN
rs682842	LRFN4	cis	multi-tissue	Pritchard
rs682842	SYT12	cis	parietal	SCAN
rs682842	CCS	cis	multi-tissue	Pritchard
rs682842	ESRRA	cis	cerebellum	SCAN
rs682842	MACROD1	cis	parietal	SCAN
rs682842	CTSF	cis	multi-tissue	Pritchard
rs682842	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs682842	ACTN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:65 , 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	chr11:66536600-66572000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:66538200-66575800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:66539800-66571400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:66544000-66609600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr11:66548400-66571400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:66550400-66571400	Weak transcription	Fetal Brain Female	brain
21	chr11:66554600-66605800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr11:66556200-66577600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr11:66556200-66577600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr11:66556200-66603000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:66556600-66571200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:66556600-66583600	Weak transcription	Fetal Stomach	stomach
27	chr11:66556600-66586000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:66556800-66589200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr11:66556800-66607400	Weak transcription	Fetal Lung	lung
30	chr11:66557000-66572400	Weak transcription	Thymus	Thymus
31	chr11:66557200-66569800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:66557200-66571000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr11:66557200-66582400	Weak transcription	NHEK	skin
34	chr11:66557400-66575600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr11:66558000-66583000	Weak transcription	Hela-S3	cervix
36	chr11:66558200-66572800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr11:66558600-66572800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr11:66560400-66569000	Weak transcription	Fetal Intestine Small	intestine
39	chr11:66560400-66575000	Weak transcription	Fetal Intestine Large	intestine
40	chr11:66560400-66595600	Weak transcription	A549	lung
41	chr11:66560400-66605400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr11:66561600-66609400	Weak transcription	Colonic Mucosa	Colon
43	chr11:66562200-66571600	Weak transcription	HMEC	breast
44	chr11:66562400-66575200	Weak transcription	Aorta	Aorta
45	chr11:66564000-66571400	Enhancers	Primary B cells from cord blood	blood
46	chr11:66564000-66580000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr11:66564200-66571600	Enhancers	Primary B cells from peripheral blood	blood
48	chr11:66565000-66605400	Weak transcription	Gastric	stomach
49	chr11:66567000-66601600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr11:66567000-66606800	Weak transcription	Brain Anterior Caudate	brain

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