Variant report

Variant	rs4370339
Chromosome Location	chr6:163767824-163767825
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	chr6:163766963..163769650-chr6:163833960..163836613,2	MCF-7	breast:
2	chr6:163757980..163760301-chr6:163766336..163768728,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL078585.1-2	chr6:163767411-163768065	XLOC_005909

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction
ENSG00000270419	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11752187	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11753466	0.89[ASN][1000 genomes]
rs12195744	0.90[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs4709711	0.89[ASN][1000 genomes]
rs760887	0.83[CHB][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4370339	LOC441177	cis	parietal	SCAN
rs4370339	PACRG	cis	brain	BrainEAC

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163745600-163773600	Enhancers	Brain Substantia Nigra	brain
2	chr6:163759000-163768400	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr6:163763200-163768000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:163763800-163768000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:163764000-163768600	Enhancers	Right Ventricle	heart
6	chr6:163764400-163769400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:163765000-163774000	Weak transcription	Spleen	Spleen
8	chr6:163765600-163773000	Enhancers	Brain Angular Gyrus	brain
9	chr6:163766000-163771400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr6:163766800-163768200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:163766800-163768400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr6:163766800-163768600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr6:163767000-163768200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:163767000-163768200	Enhancers	Fetal Brain Female	brain
15	chr6:163767000-163768400	Enhancers	Left Ventricle	heart
16	chr6:163767000-163768400	Enhancers	Right Atrium	heart
17	chr6:163767000-163768600	Enhancers	Placenta	Placenta
18	chr6:163767200-163768000	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr6:163767200-163768000	Weak transcription	Esophagus	oesophagus
20	chr6:163767200-163768000	Flanking Active TSS	HSMMtube	muscle
21	chr6:163767200-163768200	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr6:163767200-163768200	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr6:163767200-163768200	Enhancers	Fetal Brain Male	brain
24	chr6:163767200-163768600	Enhancers	Fetal Stomach	stomach
25	chr6:163767200-163770200	Enhancers	Fetal Heart	heart
26	chr6:163767400-163768000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:163767400-163768000	Active TSS	Colon Smooth Muscle	Colon
28	chr6:163767400-163768200	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr6:163767400-163768600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:163767400-163768600	Enhancers	NH-A	brain
31	chr6:163767400-163769000	Enhancers	Hela-S3	cervix
32	chr6:163767600-163768000	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr6:163767600-163768000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:163767600-163768200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr6:163767600-163768200	Flanking Active TSS	HSMM	muscle
36	chr6:163767600-163768400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr6:163767600-163770200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:163767600-163776200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:163767600-163776600	Enhancers	Brain Cingulate Gyrus	brain
40	chr6:163767800-163768000	Enhancers	Psoas Muscle	Psoas
41	chr6:163767800-163768200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:163767800-163768200	Flanking Active TSS	Fetal Muscle Trunk	muscle
43	chr6:163767800-163768400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:163767800-163768600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:163767800-163768800	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr6:163767800-163768800	Enhancers	Fetal Muscle Leg	muscle
47	chr6:163767800-163768800	Enhancers	NHDF-Ad	bronchial
48	chr6:163767800-163768800	Enhancers	NHEK	skin

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