Variant report

Variant	rs577023
Chromosome Location	chr11:66418063-66418064
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	chr11:66417428..66419556-chr11:66454925..66456744,2	K562	blood:
2	chr11:66416826..66421657-chr11:66443752..66448212,5	K562	blood:

Variant related genes	Relation type
ENSG00000173914	Chromatin interaction
ENSG00000173898	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12417769	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12577111	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12804382	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12805133	0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs1671062	0.86[JPT][hapmap]
rs1671063	0.80[JPT][hapmap]
rs1671064	0.80[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]
rs1791684	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1815739	0.80[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap]
rs2276138	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2279863	0.85[JPT][hapmap]
rs34900764	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3741363	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs474602	0.96[CEU][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs477557	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs486584	0.96[CEU][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4930387	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs498045	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs503250	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs508443	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs509556	0.88[GIH][hapmap];0.95[JPT][hapmap]
rs535211	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs540874	0.95[JPT][hapmap]
rs543191	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs556759	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs560556	0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap]
rs566673	0.81[CEU][hapmap]
rs569818	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs572846	0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap]
rs577335	0.96[CEU][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs580910	0.96[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs594313	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs608248	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs618838	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs627330	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs636128	0.81[EUR][1000 genomes]
rs6591221	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs677488	0.88[GIH][hapmap];0.95[JPT][hapmap]
rs678397	0.88[GIH][hapmap];0.95[JPT][hapmap]
rs692892	0.96[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs7925108	0.81[JPT][hapmap]
rs8432	0.86[JPT][hapmap];0.83[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs577023	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs577023	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs577023	CCS	cis	multi-tissue	Pritchard
rs577023	ACTN3	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	chr11:66409600-66418600	Strong transcription	H9 Cell Line	embryonic stem cell
3	chr11:66409800-66421600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr11:66410200-66419000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr11:66410600-66421200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr11:66411000-66421600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:66411400-66421600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:66411600-66420600	Strong transcription	NHLF	lung
9	chr11:66411600-66421200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr11:66411800-66418200	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr11:66411800-66418400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:66411800-66421000	Strong transcription	Fetal Intestine Large	intestine
13	chr11:66411800-66436200	Strong transcription	Fetal Muscle Trunk	muscle
14	chr11:66411800-66436400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:66411800-66442800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:66412000-66434400	Strong transcription	Fetal Thymus	thymus
17	chr11:66412000-66438800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:66412200-66420000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:66412200-66421200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr11:66412600-66421600	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr11:66412600-66421800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:66412600-66424800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr11:66412800-66420200	Strong transcription	Osteobl	bone
24	chr11:66412800-66420600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr11:66412800-66430600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:66412800-66435800	Strong transcription	Thymus	Thymus
27	chr11:66412800-66436800	Strong transcription	Fetal Intestine Small	intestine
28	chr11:66413000-66418400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr11:66413000-66420600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:66413000-66421200	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr11:66413000-66421600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:66413000-66423400	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr11:66413000-66435800	Strong transcription	Fetal Muscle Leg	muscle
34	chr11:66413000-66436600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr11:66413000-66440400	Strong transcription	Fetal Stomach	stomach
36	chr11:66413000-66442600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr11:66413200-66419400	Strong transcription	Fetal Kidney	kidney
38	chr11:66413400-66418800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr11:66413400-66421400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr11:66413400-66438400	Strong transcription	Dnd41	blood
41	chr11:66413600-66418200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr11:66413600-66420600	Strong transcription	GM12878-XiMat	blood
43	chr11:66413600-66420800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:66413600-66420800	Strong transcription	HSMM	muscle
45	chr11:66413600-66438400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr11:66413800-66418200	Strong transcription	Spleen	Spleen
47	chr11:66413800-66420800	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr11:66413800-66422400	Strong transcription	Duodenum Mucosa	Duodenum
49	chr11:66413800-66430400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr11:66414000-66419400	Strong transcription	Brain Germinal Matrix	brain

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