Variant report

Variant	rs1891539
Chromosome Location	chr6:119469434-119469435
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119450270..119451239-chr6:119468206..119470213,5	MCF-7	breast:
2	chr6:119256106..119257947-chr6:119468580..119471034,2	K562	blood:
3	chr6:119467858..119470789-chr6:119668770..119672252,3	K562	blood:
4	chr6:119455611..119461723-chr6:119466568..119469851,5	K562	blood:
5	chr6:119467902..119470326-chr6:119670828..119672747,2	MCF-7	breast:
6	chr6:119455611..119458749-chr6:119466100..119469942,4	K562	blood:

Variant related genes	Relation type
ENSG00000111877	Chromatin interaction
ENSG00000111885	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1150132	0.83[EUR][1000 genomes]
rs808034	0.82[AFR][1000 genomes]
rs9489607	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv886570	chr6:119450888-119600556	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1017507	chr6:119465981-119664949	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1891539	GPRC6A	cis	cerebellum	SCAN
rs1891539	TSPYL1	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119450600-119469600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:119457000-119474800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:119465800-119469800	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr6:119466000-119469800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:119466200-119469800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr6:119466200-119469800	Enhancers	HUVEC	blood vessel
7	chr6:119466200-119470200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:119466800-119470200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:119467600-119469800	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr6:119467600-119470200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:119467600-119470200	Enhancers	Hela-S3	cervix
12	chr6:119467800-119469600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:119467800-119469800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:119467800-119469800	Enhancers	Fetal Heart	heart
15	chr6:119467800-119469800	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr6:119467800-119469800	Enhancers	HSMM	muscle
17	chr6:119467800-119470200	Enhancers	Stomach Mucosa	stomach
18	chr6:119467800-119470600	Enhancers	NHLF	lung
19	chr6:119467800-119470800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr6:119467800-119470800	Enhancers	HMEC	breast
21	chr6:119468000-119469600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:119468000-119469800	Enhancers	Placenta	Placenta
23	chr6:119468000-119470200	Enhancers	Left Ventricle	heart
24	chr6:119468000-119470200	Enhancers	HSMMtube	muscle
25	chr6:119468200-119469600	Weak transcription	Brain Hippocampus Middle	brain
26	chr6:119468200-119469800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:119468200-119469800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:119468200-119469800	Enhancers	Ovary	ovary
29	chr6:119468200-119470200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:119468400-119469600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr6:119468400-119469800	Enhancers	Right Atrium	heart
32	chr6:119468400-119470000	Enhancers	Small Intestine	intestine
33	chr6:119468600-119469800	Enhancers	Fetal Muscle Leg	muscle
34	chr6:119468600-119469800	Enhancers	Placenta Amnion	Placenta Amnion
35	chr6:119468600-119469800	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr6:119468600-119469800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:119468600-119470000	Enhancers	Fetal Stomach	stomach
38	chr6:119468600-119470200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:119468600-119470800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:119468800-119469600	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr6:119468800-119469800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:119468800-119469800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:119468800-119469800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:119468800-119469800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr6:119468800-119469800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:119468800-119469800	Enhancers	Duodenum Mucosa	Duodenum
47	chr6:119468800-119469800	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr6:119468800-119469800	Enhancers	Fetal Intestine Large	intestine
49	chr6:119468800-119469800	Enhancers	Psoas Muscle	Psoas
50	chr6:119468800-119469800	Flanking Active TSS	NHDF-Ad	bronchial

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