Variant report

Variant	rs604723
Chromosome Location	chr11:100610546-100610547
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10128687	0.99[ASN][1000 genomes]
rs10431108	0.90[ASN][1000 genomes]
rs10895009	0.93[ASN][1000 genomes]
rs10895011	1.00[ASN][1000 genomes]
rs11224403	0.93[ASN][1000 genomes]
rs11224417	0.99[ASN][1000 genomes]
rs11224435	0.84[ASN][1000 genomes]
rs11224514	1.00[LWK][hapmap]
rs1216743	0.82[ASN][1000 genomes]
rs12269905	0.83[ASN][1000 genomes]
rs12286062	1.00[ASN][1000 genomes]
rs12288075	0.83[ASN][1000 genomes]
rs12291493	0.99[ASN][1000 genomes]
rs1502284	0.94[ASN][1000 genomes]
rs1847149	0.89[ASN][1000 genomes]
rs1847150	0.89[ASN][1000 genomes]
rs2298609	0.91[ASN][1000 genomes]
rs4312035	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[MEX][hapmap]
rs4495864	0.93[ASN][1000 genomes]
rs4753984	0.99[ASN][1000 genomes]
rs4754695	0.90[ASN][1000 genomes]
rs4754697	1.00[ASN][1000 genomes]
rs4754698	0.94[ASN][1000 genomes]
rs486023	0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs492237	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs607562	0.83[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs633185	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs653320	0.81[ASN][1000 genomes]
rs6590810	0.90[ASN][1000 genomes]
rs6590811	0.89[ASN][1000 genomes]
rs6590812	0.88[ASN][1000 genomes]
rs6590813	0.93[ASN][1000 genomes]
rs6590814	0.96[ASN][1000 genomes]
rs6590816	0.89[ASN][1000 genomes]
rs6590817	1.00[ASN][1000 genomes]
rs667575	0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs670401	0.81[ASN][1000 genomes]
rs67143028	0.81[ASN][1000 genomes]
rs7103397	0.99[ASN][1000 genomes]
rs7105451	0.99[ASN][1000 genomes]
rs7106603	0.94[ASN][1000 genomes]
rs7112041	0.99[ASN][1000 genomes]
rs7114867	0.99[ASN][1000 genomes]
rs7125452	0.94[ASN][1000 genomes]
rs7130275	0.99[ASN][1000 genomes]
rs7926526	0.93[ASN][1000 genomes]
rs7928576	1.00[ASN][1000 genomes]
rs7930157	1.00[ASN][1000 genomes]
rs7938194	0.85[ASN][1000 genomes]
rs7952055	1.00[ASN][1000 genomes]
rs9919648	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053430	chr11:99888390-100629136	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1042067	chr11:99889697-100629136	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1037689	chr11:99895378-100624599	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1040942	chr11:99895378-100629136	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1045190	chr11:99913193-100627395	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv541153	chr11:99913193-100627395	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv529454	chr11:99913394-100627255	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv520995	chr11:100163957-100681211	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv530643	chr11:100196082-100713156	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv898327	chr11:100569021-100631075	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs604723	DYNC2H1	cis	parietal	SCAN
rs604723	MMP8	cis	cerebellum	SCAN
rs604723	ARHGAP42	cis	Artery Tibial	GTEx
rs604723	ARHGAP42	cis	cerebellum	SCAN
rs604723	TMEM133	cis	parietal	SCAN
rs604723	TMEM133	cis	cerebellum	SCAN
rs604723	TMEM133	cis	Artery Tibial	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100590800-100611000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr11:100591000-100611000	Weak transcription	NHLF	lung
3	chr11:100591000-100611200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:100598800-100611800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:100598800-100620000	Weak transcription	Gastric	stomach
6	chr11:100599800-100619800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:100605400-100614400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr11:100606800-100610800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:100606800-100611400	Weak transcription	Primary B cells from cord blood	blood
10	chr11:100607200-100611800	Weak transcription	Left Ventricle	heart
11	chr11:100607400-100611000	Weak transcription	Right Ventricle	heart
12	chr11:100607400-100611200	Weak transcription	GM12878-XiMat	blood
13	chr11:100607400-100612200	Weak transcription	Small Intestine	intestine
14	chr11:100607400-100615600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr11:100607800-100610600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:100608200-100613000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr11:100608200-100614800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr11:100608400-100610800	Enhancers	HSMMtube	muscle
19	chr11:100608400-100611800	Enhancers	NHDF-Ad	bronchial
20	chr11:100609000-100612400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:100609000-100613000	Enhancers	Liver	Liver
22	chr11:100609000-100613200	Enhancers	Fetal Kidney	kidney
23	chr11:100609000-100613600	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr11:100609200-100612400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr11:100609200-100612400	Enhancers	Fetal Lung	lung
26	chr11:100609200-100612400	Enhancers	HSMM	muscle
27	chr11:100609200-100612800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:100609400-100613400	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr11:100609400-100613800	Enhancers	Fetal Heart	heart
30	chr11:100609600-100610600	Flanking Active TSS	A549	lung
31	chr11:100609600-100610800	Enhancers	NH-A	brain
32	chr11:100609600-100611200	Enhancers	Osteobl	bone
33	chr11:100609600-100611600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr11:100609600-100611800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:100609600-100612200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr11:100609600-100612400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr11:100609600-100612400	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr11:100609600-100613000	Enhancers	Fetal Muscle Leg	muscle
39	chr11:100609600-100613600	Enhancers	H1 Cell Line	embryonic stem cell
40	chr11:100610000-100612800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr11:100610000-100614200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr11:100610200-100611800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:100610200-100611800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:100610200-100612400	Enhancers	Fetal Intestine Large	intestine
45	chr11:100610200-100613000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr11:100610200-100613000	Enhancers	Fetal Intestine Small	intestine
47	chr11:100610200-100614400	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr11:100610200-100614800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:100610400-100610600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:100610400-100610600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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