Variant report

Variant	rs474602
Chromosome Location	chr11:66414818-66414819
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66412064..66414929-chr11:66436700..66439361,2	K562	blood:
2	chr11:66366636..66368210-chr11:66412146..66414956,2	K562	blood:
3	chr11:66414467..66416321-chr11:66424430..66427161,2	MCF-7	breast:
4	chr11:66328947..66331714-chr11:66414609..66416864,2	K562	blood:
5	chr11:66413966..66416054-chr11:66443730..66445390,2	K562	blood:
6	chr11:66095661..66097663-chr11:66414195..66416836,2	K562	blood:
7	chr11:66412976..66415260-chr11:66600626..66602387,2	K562	blood:
8	chr11:66383405..66386553-chr11:66413843..66417896,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000173914	Chromatin interaction
ENSG00000248643	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000173992	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12417769	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12577111	1.00[CEU][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12804382	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12805133	0.87[ASN][1000 genomes]
rs1791684	0.96[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1815739	0.90[YRI][hapmap]
rs2276138	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34900764	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3741363	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs477557	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs486584	1.00[CEU][hapmap];0.80[YRI][hapmap];0.90[EUR][1000 genomes]
rs4930387	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs498045	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs503250	0.96[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs535211	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs556759	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs560556	1.00[YRI][hapmap]
rs566673	0.85[CEU][hapmap]
rs572846	1.00[YRI][hapmap]
rs577023	0.96[CEU][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs577335	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs580910	1.00[CEU][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs636128	0.80[EUR][1000 genomes]
rs6591221	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs692892	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs8432	0.80[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	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
3	nsv518919	chr11:66409409-66468469	Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs474602	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs474602	CCS	cis	multi-tissue	Pritchard
rs474602	ACTN3	cis	Muscle Skeletal	GTEx
rs474602	CTD-3074O7.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66407000-66434400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:66408800-66415400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr11:66409600-66418600	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr11:66409800-66417800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr11:66409800-66421600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr11:66410200-66419000	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr11:66410400-66417200	Strong transcription	NHEK	skin
8	chr11:66410400-66417800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:66410600-66421200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr11:66410800-66416000	Strong transcription	Placenta Amnion	Placenta Amnion
11	chr11:66411000-66416400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr11:66411000-66421600	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr11:66411200-66417800	Strong transcription	NHDF-Ad	bronchial
14	chr11:66411400-66421600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:66411600-66420600	Strong transcription	NHLF	lung
16	chr11:66411600-66421200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr11:66411800-66415200	Genic enhancers	Brain Angular Gyrus	brain
18	chr11:66411800-66415400	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr11:66411800-66415600	Strong transcription	Placenta	Placenta
20	chr11:66411800-66416800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:66411800-66418200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr11:66411800-66418400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:66411800-66421000	Strong transcription	Fetal Intestine Large	intestine
24	chr11:66411800-66436200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr11:66411800-66436400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr11:66411800-66442800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:66412000-66415400	Strong transcription	Stomach Mucosa	stomach
28	chr11:66412000-66434400	Strong transcription	Fetal Thymus	thymus
29	chr11:66412000-66438800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:66412200-66415200	Strong transcription	HSMMtube	muscle
31	chr11:66412200-66420000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:66412200-66421200	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr11:66412400-66415400	Strong transcription	Primary hematopoietic stem cells	blood
34	chr11:66412400-66417000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr11:66412600-66415400	Strong transcription	Hela-S3	cervix
36	chr11:66412600-66418000	Strong transcription	Primary B cells from cord blood	blood
37	chr11:66412600-66421600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr11:66412600-66421800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr11:66412600-66424800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr11:66412800-66415400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:66412800-66415400	Strong transcription	K562	blood
42	chr11:66412800-66416800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
43	chr11:66412800-66417600	Strong transcription	HMEC	breast
44	chr11:66412800-66418000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:66412800-66418000	Strong transcription	A549	lung
46	chr11:66412800-66420200	Strong transcription	Osteobl	bone
47	chr11:66412800-66420600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr11:66412800-66430600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:66412800-66435800	Strong transcription	Thymus	Thymus
50	chr11:66412800-66436800	Strong transcription	Fetal Intestine Small	intestine

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