Variant report

Variant	rs17084
Chromosome Location	chr6:163746647-163746648
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:163700094..163703003-chr6:163745162..163748023,2	MCF-7	breast:
2	chr6:163746176..163748803-chr6:163750592..163752123,2	K562	blood:
3	chr6:163743943..163749523-chr6:163832972..163838830,12	MCF-7	breast:
4	chr6:163601211..163603439-chr6:163745434..163748650,3	MCF-7	breast:
5	chr6:163611808..163613497-chr6:163745930..163748775,2	MCF-7	breast:
6	chr6:163745590..163748829-chr6:163752310..163756417,4	MCF-7	breast:
7	chr6:163732876..163734590-chr6:163745076..163747152,2	MCF-7	breast:
8	chr6:163745999..163746681-chr6:164406770..164407469,2	MCF-7	breast:
9	chr6:163742095..163749894-chr6:163832230..163837162,13	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction
ENSG00000270419	Chromatin interaction
ENSG00000225683	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12201522	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs62428049	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67757716	0.82[ASN][1000 genomes]
rs6932724	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9356107	0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs9356108	0.81[ASN][1000 genomes]
rs9356109	0.82[ASN][1000 genomes]
rs9365552	0.86[ASN][1000 genomes]
rs9365553	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9365555	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs9458795	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs9458796	0.81[ASN][1000 genomes]
rs9458797	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9458801	0.80[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	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1022610	chr6:163591786-163814041	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv605188	chr6:163697439-163772096	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17084	MAP3K4	cis	parietal	SCAN
rs17084	QKI	cis	parietal	SCAN
rs17084	SLC22A2	cis	parietal	SCAN
rs17084	PNLDC1	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163732000-163749600	Weak transcription	Spleen	Spleen
2	chr6:163743400-163748600	Weak transcription	Left Ventricle	heart
3	chr6:163743400-163749600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:163744200-163751000	Weak transcription	Right Atrium	heart
5	chr6:163744400-163747200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr6:163744400-163747400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:163744400-163747600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:163744400-163747600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:163744600-163746800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:163744800-163746800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:163744800-163747000	Weak transcription	Pancreas	Pancrea
12	chr6:163745000-163746800	Enhancers	NHDF-Ad	bronchial
13	chr6:163745000-163753200	Weak transcription	Right Ventricle	heart
14	chr6:163745200-163767000	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr6:163745400-163746800	Enhancers	Liver	Liver
16	chr6:163745600-163773600	Enhancers	Brain Substantia Nigra	brain
17	chr6:163745800-163747400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:163745800-163754000	Enhancers	Brain Angular Gyrus	brain
19	chr6:163746000-163746800	Enhancers	Rectal Smooth Muscle	rectum
20	chr6:163746000-163747200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:163746400-163746800	Flanking Active TSS	A549	lung
22	chr6:163746400-163746800	Enhancers	HSMM	muscle
23	chr6:163746400-163746800	Enhancers	HSMMtube	muscle
24	chr6:163746400-163748600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr6:163746400-163755200	Weak transcription	Psoas Muscle	Psoas
26	chr6:163746600-163746800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:163746600-163746800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:163746600-163746800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:163746600-163747200	Enhancers	HepG2	liver
30	chr6:163746600-163747400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:163746600-163748600	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:163746600-163749400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:163746600-163750800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:163746600-163750800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:163746600-163750800	Weak transcription	Adipose Nuclei	Adipose
36	chr6:163746600-163750800	Weak transcription	NH-A	brain
37	chr6:163746600-163751000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:163746600-163751200	Weak transcription	Fetal Heart	heart
39	chr6:163746600-163753400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr6:163746600-163759400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:163746600-163759800	Enhancers	Brain Anterior Caudate	brain
42	chr6:163746600-163759800	Enhancers	Brain Hippocampus Middle	brain
43	chr6:163746600-163764400	Enhancers	Brain Cingulate Gyrus	brain

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