Variant report

Variant	rs6925979
Chromosome Location	chr6:142651052-142651053
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:142648035..142651499-chr6:142703981..142705983,3	MCF-7	breast:
2	chr6:142650601..142652419-chr6:142665853..142668621,2	MCF-7	breast:
3	chr6:142624264..142626987-chr6:142649609..142652476,2	MCF-7	breast:
4	chr6:142621734..142624141-chr6:142648345..142652169,3	MCF-7	breast:
5	chr6:142648503..142651872-chr6:142652500..142656138,3	MCF-7	breast:
6	chr6:142619918..142621591-chr6:142650811..142653503,2	MCF-7	breast:
7	chr6:142643388..142647165-chr6:142648563..142652325,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112414	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10484733	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11155241	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11155242	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11759653	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12189838	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12190271	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12197866	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12213892	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13198644	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1329705	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1329707	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17071756	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1928528	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2294775	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3817928	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4304190	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6570511	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6900087	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6900233	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6901807	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6903424	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6906468	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6912639	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6922607	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73780219	0.92[ASN][1000 genomes]
rs73780221	0.92[ASN][1000 genomes]
rs7756434	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7757571	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7765770	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7776356	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9373347	0.84[EUR][1000 genomes]
rs9403386	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142624800-142651800	Weak transcription	HSMM	muscle
2	chr6:142640400-142652000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:142640600-142651200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:142643000-142653800	Weak transcription	Fetal Heart	heart
5	chr6:142646000-142652200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:142646000-142652600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:142646400-142652400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:142646400-142652400	Enhancers	HUVEC	blood vessel
9	chr6:142649000-142655400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:142649600-142652400	Enhancers	HepG2	liver
11	chr6:142649800-142653800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:142650000-142651200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr6:142650200-142651400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr6:142650600-142652200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:142650600-142652200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:142650600-142653600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:142650600-142654200	Enhancers	HMEC	breast
18	chr6:142650800-142651200	Enhancers	Stomach Smooth Muscle	stomach
19	chr6:142650800-142651200	Flanking Active TSS	A549	lung
20	chr6:142650800-142652000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:142650800-142652400	Weak transcription	Esophagus	oesophagus
22	chr6:142650800-142652600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:142650800-142654200	Enhancers	Fetal Lung	lung
24	chr6:142650800-142654600	Enhancers	NHLF	lung
25	chr6:142651000-142652600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr6:142651000-142653200	Enhancers	NHEK	skin
27	chr6:142651000-142654600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:142651000-142656600	Enhancers	Liver	Liver

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