Variant report

Variant	rs9459254
Chromosome Location	chr6:165341545-165341546
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:164767711..164769131-chr6:165340232..165341669,7	MCF-7	breast:
2	chr6:164768200..164769032-chr6:165340931..165341635,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-QKI-5	chr6:165341449-165341714	FPKM1_group_28841_transcript_1

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12177583	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12182160	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12528995	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2093439	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2093442	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4385288	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910737	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs752485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9457026	0.84[AMR][1000 genomes]
rs9459253	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9459269	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9459277	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv605232	chr6:164994771-165401154	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv521153	chr6:165279393-165343557	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv886925	chr6:165319631-165705488	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	esv3410490	chr6:165337362-165341860	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:165333200-165346200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:165339600-165342800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:165339800-165342000	Weak transcription	Gastric	stomach
4	chr6:165340200-165341600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr6:165340800-165341600	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr6:165340800-165341600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:165340800-165344000	Active TSS	Brain Anterior Caudate	brain
8	chr6:165341000-165341600	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr6:165341000-165342000	Active TSS	Brain Cingulate Gyrus	brain
10	chr6:165341000-165342200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:165341200-165341600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:165341200-165341600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:165341200-165341600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr6:165341200-165341600	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr6:165341200-165341600	Flanking Active TSS	Fetal Kidney	kidney
16	chr6:165341200-165341600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr6:165341200-165341800	Active TSS	Fetal Muscle Trunk	muscle
18	chr6:165341200-165341800	Flanking Active TSS	HSMMtube	muscle
19	chr6:165341200-165342000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:165341200-165342000	Active TSS	Fetal Brain Male	brain
21	chr6:165341200-165342000	Active TSS	Psoas Muscle	Psoas
22	chr6:165341200-165342000	Active TSS	Osteobl	bone
23	chr6:165341200-165342200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr6:165341200-165342200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:165341200-165342200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:165341200-165342200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr6:165341200-165342200	Flanking Active TSS	HSMM	muscle
28	chr6:165341200-165342200	Active TSS	NH-A	brain
29	chr6:165341200-165342600	Active TSS	Brain Germinal Matrix	brain
30	chr6:165341200-165342600	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr6:165341200-165342800	Active TSS	Brain Angular Gyrus	brain
32	chr6:165341200-165342800	Active TSS	Brain Hippocampus Middle	brain
33	chr6:165341200-165343000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:165341200-165343200	Active TSS	Fetal Brain Female	brain
35	chr6:165341400-165341600	Flanking Active TSS	Brain Substantia Nigra	brain
36	chr6:165341400-165341600	Enhancers	Fetal Stomach	stomach
37	chr6:165341400-165341800	Active TSS	Fetal Muscle Leg	muscle
38	chr6:165341400-165342000	Active TSS	Stomach Smooth Muscle	stomach

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