Variant report

Variant	rs541668
Chromosome Location	chr6:44243050-44243051
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:44241706..44244542-chr6:44247221..44249116,2	K562	blood:
2	chr6:44235774..44239606-chr6:44242951..44245858,3	MCF-7	breast:
3	chr6:44242284..44246953-chr6:44248645..44251734,5	K562	blood:
4	chr6:44242956..44244489-chr6:44249493..44251031,2	K562	blood:

Variant related genes	Relation type
ENSG00000178233	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs161706	0.83[AMR][1000 genomes]
rs324136	0.83[AMR][1000 genomes]
rs324141	0.89[AMR][1000 genomes]
rs325009	0.83[AMR][1000 genomes]
rs484757	0.89[AMR][1000 genomes]
rs505617	0.84[AMR][1000 genomes]
rs511088	0.89[AMR][1000 genomes]
rs568902	0.83[AMR][1000 genomes]
rs7740535	0.83[AMR][1000 genomes]
rs865027	0.89[AMR][1000 genomes]
rs9472241	0.84[AMR][1000 genomes]
rs9472243	0.83[AMR][1000 genomes]
rs9472244	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv603003	chr6:44191920-44253765	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv524398	chr6:44200953-44253765	Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
9	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
10	nsv885857	chr6:44223010-44250165	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
11	esv3422155	chr6:44242599-44245147	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44239000-44243600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:44239000-44243600	Weak transcription	Right Atrium	heart
3	chr6:44239400-44243600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:44239600-44243200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:44239600-44244600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:44239600-44247600	Enhancers	Fetal Brain Male	brain
7	chr6:44240400-44243600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:44240800-44243600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:44240800-44245000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:44241000-44243600	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr6:44241000-44244200	Strong transcription	Brain Germinal Matrix	brain
12	chr6:44241200-44252200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:44242200-44243200	Strong transcription	Fetal Brain Female	brain
14	chr6:44242200-44243200	Bivalent Enhancer	HepG2	liver
15	chr6:44242400-44244000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:44242400-44245200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:44243000-44243200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:44243000-44243200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:44243000-44243200	Bivalent Enhancer	Ovary	ovary
20	chr6:44243000-44243400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:44243000-44243400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:44243000-44243400	Bivalent Enhancer	Right Ventricle	heart
23	chr6:44243000-44244000	Bivalent/Poised TSS	NHEK	skin
24	chr6:44243000-44244400	Enhancers	Lung	lung
25	chr6:44243000-44244400	Bivalent Enhancer	Spleen	Spleen

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