Variant report

Variant	rs1406935
Chromosome Location	chr6:132557755-132557756
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	6:132269655-132282174..6:132556576-132559814	GM12878	blood:
2	6:132182612-132191683..6:132556576-132559814	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000118523	Chromatin interaction
ENSG00000227220	Chromatin interaction
ENSG00000197594	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10457585	0.81[AFR][1000 genomes]
rs1321261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1321279	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs1321280	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1406932	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1406939	0.82[CEU][hapmap]
rs1406940	0.84[JPT][hapmap]
rs1535196	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs1535197	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1535198	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3927419	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4142807	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs4142808	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs6569777	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs6569779	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569788	0.83[EUR][1000 genomes]
rs6933036	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6935755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7739499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7742430	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs7760956	0.86[JPT][hapmap]
rs9375866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9385597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388967	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9402390	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs9402391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9402392	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9483414	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs9493239	0.82[CEU][hapmap];0.86[JPT][hapmap]

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	esv2762616	chr6:132404708-132584324	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1024527	chr6:132532941-132571889	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:132552200-132562400	Weak transcription	Psoas Muscle	Psoas
2	chr6:132553800-132557800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:132555600-132558200	Enhancers	Muscle Satellite Cultured Cells	--
4	chr6:132555600-132558400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:132556200-132558000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:132556400-132558600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:132556600-132557800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:132556600-132558000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:132556600-132558200	Enhancers	NHLF	lung
10	chr6:132556600-132558200	Enhancers	Osteobl	bone
11	chr6:132556800-132558200	Enhancers	HMEC	breast
12	chr6:132556800-132558200	Enhancers	HSMMtube	muscle
13	chr6:132556800-132558400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:132557000-132558000	Enhancers	HSMM	muscle
15	chr6:132557000-132558200	Enhancers	NH-A	brain
16	chr6:132557000-132558400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:132557000-132558800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr6:132557200-132558400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr6:132557200-132558600	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr6:132557200-132558800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:132557400-132557800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:132557400-132557800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:132557400-132558000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:132557400-132558600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr6:132557600-132557800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr6:132557600-132558400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:132557600-132559000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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