Variant report

Variant	rs7947408
Chromosome Location	chr11:107936320-107936321
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	chr11:107930379..107933098-chr11:107935070..107937176,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11212474	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11212475	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11600706	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11600740	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11602683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605419	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605878	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11607758	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11822270	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11822609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11822651	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11825746	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11825936	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11828176	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17107675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17617000	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3741053	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3781870	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4565865	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58243661	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6588998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7103534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7107097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7118335	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7125285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130647	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73555359	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73555372	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73555391	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73557106	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73557111	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73557122	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73557155	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73557188	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7927717	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7929383	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7936826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943669	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1049524	chr11:107540937-107954011	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv2750980	chr11:107720941-107970986	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1047984	chr11:107794729-107950746	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	esv3372573	chr11:107880365-108022895	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7947408	ACAT1	cis	parietal	SCAN
rs7947408	ACAT1	cis	multi-tissue	Pritchard
rs7947408	ACAT1	Cis_1M	lymphoblastoid	RTeQTL
rs7947408	GRIA4	cis	parietal	SCAN
rs7947408	LAYN	cis	parietal	SCAN
rs7947408	ACAT1	cis	cerebellum	SCAN
rs7947408	NPAT	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107884400-107942000	Weak transcription	Esophagus	oesophagus
2	chr11:107890800-107975200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:107891000-107965800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr11:107891200-107966200	Weak transcription	Small Intestine	intestine
5	chr11:107896600-107962000	Weak transcription	Right Ventricle	heart
6	chr11:107902600-107974400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:107903600-107957600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr11:107903800-107938000	Strong transcription	Dnd41	blood
9	chr11:107906800-107942000	Weak transcription	Aorta	Aorta
10	chr11:107906800-107945600	Weak transcription	Spleen	Spleen
11	chr11:107906800-107947000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:107908200-107964000	Weak transcription	Fetal Heart	heart
13	chr11:107908400-107980600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:107908600-107940800	Weak transcription	A549	lung
15	chr11:107908800-107939600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr11:107909200-107941000	Weak transcription	NHLF	lung
17	chr11:107914800-107937800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:107914800-107955800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr11:107916000-107938200	Strong transcription	Adipose Nuclei	Adipose
20	chr11:107916200-107938600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:107917000-107940200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr11:107917800-107937600	Strong transcription	Fetal Muscle Leg	muscle
23	chr11:107918200-107942000	Weak transcription	Gastric	stomach
24	chr11:107918200-107946200	Weak transcription	Pancreas	Pancrea
25	chr11:107921000-107938600	Strong transcription	Fetal Intestine Large	intestine
26	chr11:107922400-107936600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr11:107922600-107938000	Strong transcription	Fetal Thymus	thymus
28	chr11:107923800-107936600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr11:107923800-107965800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr11:107924200-107940800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr11:107924400-107941000	Weak transcription	HUVEC	blood vessel
32	chr11:107924800-107938000	Strong transcription	Primary T cells from cord blood	blood
33	chr11:107925800-107936600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr11:107926000-107936600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr11:107926200-107950200	Weak transcription	HMEC	breast
36	chr11:107927000-107950400	Weak transcription	Colonic Mucosa	Colon
37	chr11:107928000-107940400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr11:107928200-107937400	Weak transcription	Hela-S3	cervix
39	chr11:107928200-107940400	Weak transcription	Colon Smooth Muscle	Colon
40	chr11:107928200-107941400	Weak transcription	Brain Germinal Matrix	brain
41	chr11:107928200-107953600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr11:107928200-107962000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr11:107928200-107985200	Weak transcription	Psoas Muscle	Psoas
44	chr11:107928400-107937200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr11:107928400-107940800	Weak transcription	NHDF-Ad	bronchial
46	chr11:107928400-107946000	Weak transcription	HSMMtube	muscle
47	chr11:107928400-107950200	Weak transcription	Fetal Brain Male	brain
48	chr11:107928400-107950400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:107928600-107944400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr11:107928600-107944400	Weak transcription	HepG2	liver

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