Variant report

Variant	rs3858412
Chromosome Location	chr11:100663301-100663302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10791427	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11224435	0.81[ASN][1000 genomes]
rs11224461	0.87[ASN][1000 genomes]
rs11224474	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11823529	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417529	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12419467	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12419937	0.91[ASN][1000 genomes]
rs12793858	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12801715	0.85[ASN][1000 genomes]
rs17651772	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2155140	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35472062	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35473622	0.84[ASN][1000 genomes]
rs3858410	0.89[ASN][1000 genomes]
rs4754701	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs509358	0.81[ASN][1000 genomes]
rs536090	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58051655	0.81[ASN][1000 genomes]
rs582409	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs588615	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs595030	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs600906	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs607890	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs612090	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs614615	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626558	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6590820	0.87[ASN][1000 genomes]
rs660736	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs662449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs685611	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100645600-100679800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr11:100645800-100679600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:100654400-100671200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr11:100656600-100679600	Weak transcription	Fetal Lung	lung
5	chr11:100656800-100668800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr11:100657000-100675600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:100659600-100663400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr11:100659800-100663400	Enhancers	A549	lung
9	chr11:100660000-100663400	Enhancers	NHEK	skin
10	chr11:100660400-100669400	Weak transcription	Placenta	Placenta
11	chr11:100660400-100679400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:100660400-100679600	Weak transcription	Stomach Mucosa	stomach
13	chr11:100660400-100683600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:100660600-100667000	Weak transcription	NH-A	brain
15	chr11:100660600-100668400	Weak transcription	HSMMtube	muscle
16	chr11:100660600-100671000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr11:100660600-100675600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr11:100660600-100679600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr11:100660600-100679600	Weak transcription	HSMM	muscle
20	chr11:100660600-100680000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:100660600-100680400	Weak transcription	Left Ventricle	heart
22	chr11:100661000-100664200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr11:100661000-100671800	Weak transcription	Liver	Liver
24	chr11:100661800-100663400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:100662000-100663800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr11:100662000-100669400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr11:100662600-100663400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr11:100662600-100679600	Weak transcription	Fetal Heart	heart
29	chr11:100662800-100663400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr11:100662800-100663400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr11:100662800-100664000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:100662800-100665000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:100663000-100663400	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr11:100663000-100664000	Weak transcription	HUVEC	blood vessel
35	chr11:100663000-100668000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr11:100663000-100691800	Weak transcription	Fetal Muscle Leg	muscle
37	chr11:100663200-100663400	Enhancers	Fetal Kidney	kidney
38	chr11:100663200-100663800	Weak transcription	Adipose Nuclei	Adipose
39	chr11:100663200-100667800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr11:100663200-100679600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr11:100663200-100679600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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