Variant report

Variant	rs275349
Chromosome Location	chr6:150967805-150967806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150966591..150968646-chr6:150981306..150983343,2	MCF-7	breast:
2	chr6:150960489..150962367-chr6:150966319..150968724,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1388912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs275343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs275344	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs275345	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs6557549	0.94[JPT][hapmap];0.98[LWK][hapmap];0.81[MEX][hapmap];0.98[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7769605	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7775858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9372081	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9384570	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9384571	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]

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	nsv886772	chr6:150743364-151024280	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv886774	chr6:150931131-150983318	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1030326	chr6:150967665-151641372	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs275349	DYM	trans	lymphoblastoid	RTeQTL
rs275349	IYD	cis	cerebellum	SCAN
rs275349	LATS1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150955800-150972400	Weak transcription	Fetal Stomach	stomach
2	chr6:150958200-150971200	Weak transcription	Left Ventricle	heart
3	chr6:150959800-150987400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:150960400-150980600	Weak transcription	Stomach Mucosa	stomach
5	chr6:150961600-150975200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:150961600-150980200	Weak transcription	Lung	lung
7	chr6:150961800-150972600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:150963000-150979200	Weak transcription	Fetal Lung	lung
9	chr6:150963800-150974200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:150964000-150974000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:150964200-150975200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:150964600-150971200	Weak transcription	Brain Substantia Nigra	brain
13	chr6:150964600-150977400	Weak transcription	Small Intestine	intestine
14	chr6:150964600-150979200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:150964600-150980000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:150964800-150975400	Weak transcription	Fetal Kidney	kidney
17	chr6:150964800-150987400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:150965000-150971400	Weak transcription	Fetal Thymus	thymus
19	chr6:150965000-150971600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr6:150965000-150974600	Weak transcription	Thymus	Thymus
21	chr6:150967000-150968000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr6:150967000-150968800	Enhancers	Brain Germinal Matrix	brain
23	chr6:150967400-150975400	Weak transcription	Esophagus	oesophagus
24	chr6:150967800-150968200	Weak transcription	Primary B cells from cord blood	blood
25	chr6:150967800-150968400	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr6:150967800-150968800	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr6:150967800-150974400	Weak transcription	Spleen	Spleen
28	chr6:150967800-150980200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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