Variant report

Variant	rs3819722
Chromosome Location	chr6:119507585-119507586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119506495..119510474-chr6:119512105..119518415,7	K562	blood:
2	chr6:119503709..119505981-chr6:119506117..119508787,2	MCF-7	breast:
3	chr6:119506358..119507997-chr6:119521018..119522691,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11964347	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11964813	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11967793	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11967806	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11970393	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11970420	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12528343	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3734383	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756943	0.89[GIH][hapmap]
rs3819723	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58744690	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6569053	0.85[ASN][1000 genomes]
rs760784	0.88[AFR][1000 genomes]
rs760786	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs873536	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs873537	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs926358	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs926359	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[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	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
4	nsv886571	chr6:119494199-119517239	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3819722	PIK3CG	trans	parietal	SCAN
rs3819722	TRDN	cis	cerebellum	SCAN
rs3819722	TSPYL1	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119491800-119531200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:119492200-119527800	Weak transcription	NHEK	skin
3	chr6:119492400-119524200	Weak transcription	Fetal Stomach	stomach
4	chr6:119493600-119518000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:119494000-119523600	Weak transcription	GM12878-XiMat	blood
6	chr6:119494600-119547400	Weak transcription	Esophagus	oesophagus
7	chr6:119494800-119526200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:119495400-119522000	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:119495600-119522200	Weak transcription	Fetal Kidney	kidney
10	chr6:119497000-119512600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:119497000-119524000	Weak transcription	NHLF	lung
12	chr6:119497000-119524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:119497000-119524400	Weak transcription	Small Intestine	intestine
14	chr6:119497200-119518600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:119497400-119507600	Weak transcription	Aorta	Aorta
16	chr6:119498000-119536600	Weak transcription	Fetal Heart	heart
17	chr6:119498200-119527400	Strong transcription	Liver	Liver
18	chr6:119498600-119508400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:119498600-119508600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:119498600-119517600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:119498600-119531400	Strong transcription	HepG2	liver
22	chr6:119498800-119526800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:119499000-119517200	Strong transcription	Primary hematopoietic stem cells	blood
24	chr6:119499400-119516200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:119499400-119518200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:119499400-119525400	Weak transcription	NH-A	brain
27	chr6:119499600-119524000	Weak transcription	Brain Anterior Caudate	brain
28	chr6:119499800-119524400	Weak transcription	Right Ventricle	heart
29	chr6:119500000-119509600	Weak transcription	Fetal Thymus	thymus
30	chr6:119500800-119515800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:119501200-119522200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:119501400-119507600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:119501600-119513200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:119501600-119515000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:119501600-119518000	Weak transcription	Thymus	Thymus
36	chr6:119501600-119524200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:119501800-119509600	Weak transcription	Primary T cells from cord blood	blood
38	chr6:119502000-119509400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr6:119502000-119510000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr6:119502000-119515400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr6:119502000-119523800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr6:119502000-119523800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr6:119502400-119525800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:119502600-119507600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr6:119502600-119526800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr6:119503200-119512000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:119503400-119539800	Weak transcription	Gastric	stomach
48	chr6:119503800-119524200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr6:119504200-119507600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:119504200-119515400	Strong transcription	Fetal Intestine Large	intestine

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