Variant report

Variant	rs56125439
Chromosome Location	chr6:79861863-79861864
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:79861129..79863468-chr6:79865472..79868083,2	MCF-7	breast:
2	chr6:79786929..79788709-chr6:79859954..79862909,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146247	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10484945	1.00[EUR][1000 genomes]
rs1335536	1.00[EUR][1000 genomes]
rs16890581	1.00[EUR][1000 genomes]
rs35686657	1.00[EUR][1000 genomes]
rs55654065	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55779333	1.00[EUR][1000 genomes]
rs55786726	1.00[EUR][1000 genomes]
rs56177348	1.00[EUR][1000 genomes]
rs56735945	1.00[EUR][1000 genomes]
rs56926933	1.00[EUR][1000 genomes]
rs57810626	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58284219	1.00[EUR][1000 genomes]
rs59392118	1.00[EUR][1000 genomes]
rs60132767	1.00[EUR][1000 genomes]
rs60420555	1.00[EUR][1000 genomes]
rs61411441	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61649774	1.00[EUR][1000 genomes]
rs6904575	1.00[EUR][1000 genomes]
rs6917206	1.00[EUR][1000 genomes]
rs73464119	1.00[EUR][1000 genomes]
rs73464137	1.00[EUR][1000 genomes]
rs73464147	1.00[EUR][1000 genomes]
rs73466210	1.00[EUR][1000 genomes]
rs73466218	1.00[EUR][1000 genomes]
rs73466221	1.00[EUR][1000 genomes]
rs73466224	1.00[EUR][1000 genomes]
rs73466237	0.85[AFR][1000 genomes]
rs73466240	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73466263	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73466271	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73466273	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73466290	1.00[EUR][1000 genomes]
rs73764092	1.00[EUR][1000 genomes]
rs73767528	1.00[EUR][1000 genomes]
rs7762406	1.00[EUR][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	nsv830706	chr6:79825910-79994878	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79858600-79862400	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr6:79859400-79864400	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr6:79859600-79863800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:79860000-79862400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:79860000-79862800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:79861400-79862200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:79861400-79862600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:79861400-79862800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:79861400-79863000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:79861400-79864200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr6:79861600-79862000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:79861600-79862000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:79861600-79862000	Enhancers	HepG2	liver
14	chr6:79861600-79862200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr6:79861600-79862200	Enhancers	Brain Cingulate Gyrus	brain
16	chr6:79861600-79862200	Enhancers	Brain Substantia Nigra	brain
17	chr6:79861600-79862400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr6:79861600-79862400	Enhancers	HMEC	breast
19	chr6:79861600-79862800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr6:79861800-79862000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:79861800-79862000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:79861800-79862200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:79861800-79862200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr6:79861800-79862200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:79861800-79862200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:79861800-79862200	Enhancers	A549	lung
27	chr6:79861800-79862200	Enhancers	K562	blood
28	chr6:79861800-79862400	Enhancers	Brain Hippocampus Middle	brain
29	chr6:79861800-79862400	Enhancers	Psoas Muscle	Psoas

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