Variant report

Variant	rs9972386
Chromosome Location	chr15:82454283-82454284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10152239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152695	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12323987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439569	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12442862	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13380011	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17269323	1.00[CEU][hapmap];0.89[MEX][hapmap]
rs28463928	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28715426	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4778672	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap]
rs57264750	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57598148	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58227679	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58303451	0.88[AMR][1000 genomes]
rs60341871	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60439528	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61094688	0.99[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61413136	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61421773	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61433916	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167816	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs74030944	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74030948	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74030949	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457212	chr15:82454283-82573255	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv570243	chr15:82454283-82573255	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9972386	DKFZp666G057	cis	multi-tissue	Pritchard
rs9972386	DKFZp666G057	Cis_1M	lymphoblastoid	RTeQTL
rs9972386	LOC283726	cis	multi-tissue	Pritchard
rs9972386	FAM154B	cis	multi-tissue	Pritchard
rs9972386	FAM154B	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82419200-82470600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:82420000-82457000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:82420400-82458400	Weak transcription	HepG2	liver
4	chr15:82423200-82454800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:82426000-82457000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:82427600-82456600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:82430400-82455200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr15:82431200-82455000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:82431200-82461200	Weak transcription	Small Intestine	intestine
10	chr15:82432600-82454800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr15:82432600-82454800	Weak transcription	Colon Smooth Muscle	Colon
12	chr15:82432600-82457800	Weak transcription	Fetal Lung	lung
13	chr15:82432600-82476400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:82432600-82552800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr15:82433400-82458400	Weak transcription	Fetal Kidney	kidney
16	chr15:82438400-82456800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr15:82439400-82455400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:82439800-82454800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:82439800-82465600	Weak transcription	K562	blood
20	chr15:82440400-82455000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:82440400-82458200	Weak transcription	HUVEC	blood vessel
22	chr15:82441400-82469600	Weak transcription	Fetal Brain Male	brain
23	chr15:82442800-82454400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:82443000-82454800	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:82443400-82457000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr15:82444000-82455800	Weak transcription	Fetal Brain Female	brain
27	chr15:82444200-82454400	Weak transcription	Aorta	Aorta
28	chr15:82444200-82454400	Weak transcription	Spleen	Spleen
29	chr15:82444400-82454600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:82444400-82454800	Weak transcription	Brain Angular Gyrus	brain
31	chr15:82444400-82454800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr15:82444400-82455000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:82444400-82455000	Weak transcription	Right Ventricle	heart
34	chr15:82444400-82465200	Weak transcription	Brain Germinal Matrix	brain
35	chr15:82444600-82454400	Weak transcription	Fetal Muscle Leg	muscle
36	chr15:82444600-82454400	Weak transcription	Fetal Stomach	stomach
37	chr15:82444600-82454400	Weak transcription	Left Ventricle	heart
38	chr15:82444600-82454800	Weak transcription	Brain Anterior Caudate	brain
39	chr15:82444600-82454800	Weak transcription	Brain Substantia Nigra	brain
40	chr15:82444600-82454800	Weak transcription	Ovary	ovary
41	chr15:82444600-82455000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr15:82444600-82455000	Weak transcription	Placenta	Placenta
43	chr15:82444600-82455000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr15:82444600-82455200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr15:82444600-82456600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr15:82444600-82458000	Weak transcription	NHLF	lung
47	chr15:82444600-82495800	Weak transcription	Fetal Intestine Small	intestine
48	chr15:82444800-82454400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr15:82444800-82454400	Weak transcription	Fetal Thymus	thymus
50	chr15:82446400-82456400	Strong transcription	Monocytes-CD14+_RO01746	blood

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