Variant report

Variant	rs3801357
Chromosome Location	chr7:79840111-79840112
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	chr7:79826630..79828423-chr7:79838605..79841160,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10234223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10241877	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10247757	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10248135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10268519	0.82[GIH][hapmap]
rs10268773	0.83[GIH][hapmap]
rs10276981	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10278243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706718	0.84[ASN][1000 genomes]
rs12721455	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17245731	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17806203	0.82[GIH][hapmap]
rs2366255	0.86[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs28647788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4731273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67096317	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs73151419	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[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	nsv429785	chr7:79589749-80177049	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1024312	chr7:79832637-80004812	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1029180	chr7:79832637-80017560	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3801357	GNAI1	cis	cerebellum	SCAN
rs3801357	GNAI1	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79801800-79840400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:79807800-79842000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:79809600-79847600	Weak transcription	HUVEC	blood vessel
4	chr7:79811600-79845000	Weak transcription	Primary T cells from cord blood	blood
5	chr7:79814200-79842600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:79815000-79848200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr7:79815000-79850200	Weak transcription	Lung	lung
8	chr7:79815200-79859600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr7:79816200-79846800	Weak transcription	Esophagus	oesophagus
10	chr7:79816400-79854800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:79817000-79841000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr7:79817000-79842400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:79817000-79851200	Weak transcription	Aorta	Aorta
14	chr7:79820600-79847000	Weak transcription	NHLF	lung
15	chr7:79820600-79853800	Weak transcription	Left Ventricle	heart
16	chr7:79825000-79847400	Weak transcription	Pancreas	Pancrea
17	chr7:79825200-79844000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr7:79825400-79856600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr7:79827000-79842600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr7:79827400-79842200	Weak transcription	NH-A	brain
21	chr7:79828000-79845600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr7:79828200-79842200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr7:79829200-79846000	Weak transcription	Right Ventricle	heart
24	chr7:79829200-79853000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr7:79829400-79845800	Weak transcription	Psoas Muscle	Psoas
26	chr7:79829600-79841200	Weak transcription	Fetal Muscle Leg	muscle
27	chr7:79830400-79840400	Weak transcription	Fetal Brain Male	brain
28	chr7:79830600-79842400	Weak transcription	Fetal Kidney	kidney
29	chr7:79830800-79848400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr7:79831000-79840400	Weak transcription	Ovary	ovary
31	chr7:79831000-79840800	Weak transcription	Fetal Intestine Small	intestine
32	chr7:79831000-79848200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr7:79831000-79853800	Weak transcription	Gastric	stomach
34	chr7:79831600-79850800	Weak transcription	Fetal Stomach	stomach
35	chr7:79831800-79840200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr7:79831800-79861200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr7:79832200-79840400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr7:79832400-79840200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr7:79832400-79855000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr7:79833200-79840200	Weak transcription	Hela-S3	cervix
41	chr7:79834000-79840200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr7:79834000-79840400	Weak transcription	Placenta	Placenta
43	chr7:79834000-79841200	Weak transcription	Brain Germinal Matrix	brain
44	chr7:79834000-79850600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr7:79834200-79840200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr7:79834600-79841400	Weak transcription	Fetal Brain Female	brain
47	chr7:79834800-79841000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr7:79835200-79842000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr7:79835600-79840400	Genic enhancers	Fetal Lung	lung
50	chr7:79836000-79859600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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