Variant report

Variant	rs9320690
Chromosome Location	chr6:119770906-119770907
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	chr6:119770080..119773062-chr6:119774639..119776880,2	K562	blood:
2	chr6:119769489..119771005-chr6:119951026..119953518,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11153809	0.80[CEU][hapmap]
rs12194357	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12527248	0.82[EUR][1000 genomes]
rs1295383	0.81[EUR][1000 genomes]
rs1295384	0.81[EUR][1000 genomes]
rs2036257	0.84[CEU][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2144236	0.80[EUR][1000 genomes]
rs2357379	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35147613	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35305935	0.86[EUR][1000 genomes]
rs6569076	0.80[EUR][1000 genomes]
rs6915559	0.80[CEU][hapmap]
rs6915947	0.80[CEU][hapmap]
rs6918913	0.80[CEU][hapmap]
rs6927955	0.80[CEU][hapmap]
rs6936020	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6936790	0.80[EUR][1000 genomes]
rs715373	0.80[CEU][hapmap]
rs715374	0.80[CEU][hapmap]
rs7741003	0.80[CEU][hapmap]
rs7753315	0.80[CEU][hapmap]
rs9320689	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9374795	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9374796	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489681	0.80[CEU][hapmap]
rs9489686	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1027904	chr6:119709488-120001986	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv533518	chr6:119712186-119998618	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3442553	chr6:119742069-120076777	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv1845804	chr6:119747112-119771715	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9320690	GPRC6A	cis	cerebellum	SCAN
rs9320690	FAM162B	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119760600-119774800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:119763400-119772200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr6:119763600-119772200	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr6:119768000-119771200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr6:119768200-119774000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:119768200-119780400	Weak transcription	Aorta	Aorta
7	chr6:119768400-119771200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:119768800-119775600	Weak transcription	Brain Anterior Caudate	brain
9	chr6:119770000-119771400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr6:119770000-119771400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:119770000-119771400	Enhancers	GM12878-XiMat	blood
12	chr6:119770000-119772000	Enhancers	Primary B cells from cord blood	blood
13	chr6:119770200-119771400	Enhancers	Primary B cells from peripheral blood	blood
14	chr6:119770200-119771400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:119770200-119771400	Enhancers	Duodenum Mucosa	Duodenum
16	chr6:119770200-119771400	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr6:119770200-119771400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr6:119770200-119772200	Enhancers	Fetal Intestine Large	intestine
19	chr6:119770400-119771400	Enhancers	Primary hematopoietic stem cells	blood
20	chr6:119770400-119771400	Enhancers	Fetal Intestine Small	intestine
21	chr6:119770400-119774600	Weak transcription	Adipose Nuclei	Adipose
22	chr6:119770400-119774800	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:119770600-119771200	Enhancers	Stomach Mucosa	stomach
24	chr6:119770600-119774200	Weak transcription	Spleen	Spleen
25	chr6:119770600-119774400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:119770600-119776000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:119770800-119771000	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr6:119770800-119774200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:119770800-119774400	Weak transcription	Dnd41	blood
30	chr6:119770800-119780000	Weak transcription	Gastric	stomach

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