Variant report

Variant	rs7760002
Chromosome Location	chr6:163683522-163683523
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:163619302..163621852-chr6:163683443..163685486,2	MCF-7	breast:
2	chr6:163682473..163685111-chr6:163834229..163835795,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL078585.1-10	chr6:163681777-163684612	refGeneNc_1043_NR_033862

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction
ENSG00000270419	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11753486	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4579329	0.81[AMR][1000 genomes]
rs4709687	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62427989	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915137	0.81[AMR][1000 genomes]
rs9365546	0.81[AMR][1000 genomes]
rs9456849	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1026490	chr6:163133433-163705708	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv869286	chr6:163146342-163697445	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7760002	PRR18	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163680000-163683600	Enhancers	Brain Angular Gyrus	brain
2	chr6:163680000-163686600	Enhancers	Fetal Heart	heart
3	chr6:163680800-163683600	Enhancers	Fetal Brain Male	brain
4	chr6:163681200-163685400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:163681400-163684200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:163681400-163684200	Weak transcription	Gastric	stomach
7	chr6:163681400-163685200	Weak transcription	Pancreas	Pancrea
8	chr6:163681800-163683800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:163681800-163685000	Weak transcription	Liver	Liver
10	chr6:163682000-163683600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:163682000-163685400	Weak transcription	Esophagus	oesophagus
12	chr6:163682000-163686200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:163682000-163686400	Enhancers	Brain Cingulate Gyrus	brain
14	chr6:163682000-163686400	Enhancers	Brain Substantia Nigra	brain
15	chr6:163682000-163701600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:163682200-163683600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:163682200-163683800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:163682200-163684000	Weak transcription	Adipose Nuclei	Adipose
19	chr6:163682200-163684000	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:163682200-163684200	Enhancers	Brain Anterior Caudate	brain
21	chr6:163682200-163684200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr6:163682200-163684200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:163682200-163684800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:163682200-163685400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr6:163682200-163685400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:163682200-163685600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:163682200-163685800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:163682200-163686600	Enhancers	Brain Hippocampus Middle	brain
29	chr6:163682600-163683800	Weak transcription	Left Ventricle	heart
30	chr6:163682600-163683800	Weak transcription	Right Ventricle	heart
31	chr6:163682600-163688000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:163682800-163683600	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr6:163682800-163683600	Weak transcription	Right Atrium	heart
34	chr6:163682800-163683800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:163682800-163684200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:163682800-163684400	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr6:163682800-163686400	Enhancers	H1 Cell Line	embryonic stem cell
38	chr6:163683000-163683800	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr6:163683000-163684200	Weak transcription	Fetal Brain Female	brain
40	chr6:163683200-163684200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:163683200-163686400	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr6:163683400-163683600	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr6:163683400-163683600	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr6:163683400-163685800	Enhancers	Brain Germinal Matrix	brain

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