Variant report

Variant	rs16958836
Chromosome Location	chr15:34439170-34439171
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11072998	0.81[ASN][1000 genomes]
rs11852537	0.97[YRI][hapmap]
rs11854686	0.90[YRI][hapmap]
rs11857684	0.97[YRI][hapmap]
rs12594077	0.85[ASN][1000 genomes]
rs16958829	0.82[ASN][1000 genomes]
rs16958835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978810	0.90[YRI][hapmap]
rs2339368	0.82[ASN][1000 genomes]
rs2339369	0.81[ASN][1000 genomes]
rs56936283	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57699120	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57715967	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59611916	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495558	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166360	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168761	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs7172480	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7174442	0.96[YRI][hapmap]
rs7175168	0.82[ASN][1000 genomes]
rs7178002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap]
rs7178203	0.96[YRI][hapmap]
rs7178988	0.90[YRI][hapmap]
rs7181687	0.89[YRI][hapmap]
rs7181902	0.89[YRI][hapmap]
rs73376156	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73376164	0.85[ASN][1000 genomes]
rs73376168	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73376178	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73376181	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73376192	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73376193	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73376196	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73378126	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73378144	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73380107	0.82[ASN][1000 genomes]
rs8025730	0.93[YRI][hapmap];0.83[ASN][1000 genomes]
rs8031102	0.83[ASN][1000 genomes]
rs8036791	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8040071	0.83[CHB][hapmap]
rs8040732	0.85[CHB][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035579	chr15:34363159-34501115	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16958836	NOP10	cis	Esophagus Muscularis	GTEx
rs16958836	NOP10	cis	Heart Left Ventricle	GTEx
rs16958836	NOP10	cis	Muscle Skeletal	GTEx
rs16958836	NOP10	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34416200-34439200	Weak transcription	HUVEC	blood vessel
2	chr15:34417600-34439400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr15:34419400-34441800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:34424400-34446400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:34425800-34439800	Weak transcription	Brain Hippocampus Middle	brain
6	chr15:34427800-34446400	Weak transcription	Psoas Muscle	Psoas
7	chr15:34428000-34441800	Weak transcription	Esophagus	oesophagus
8	chr15:34428400-34439800	Weak transcription	Thymus	Thymus
9	chr15:34428800-34442400	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:34429000-34442400	Weak transcription	Aorta	Aorta
11	chr15:34429000-34444400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr15:34429200-34446200	Strong transcription	Placenta	Placenta
13	chr15:34429400-34439600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:34429400-34439600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:34429400-34445400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:34429400-34445600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:34429400-34445800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:34429600-34444800	Strong transcription	Adipose Nuclei	Adipose
19	chr15:34429600-34446400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr15:34429800-34446400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:34429800-34456800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:34430200-34439800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:34430200-34440200	Weak transcription	Ovary	ovary
24	chr15:34430200-34443000	Weak transcription	Fetal Brain Male	brain
25	chr15:34430200-34443800	Weak transcription	GM12878-XiMat	blood
26	chr15:34430200-34445600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr15:34430200-34446000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:34430400-34443000	Weak transcription	Fetal Heart	heart
29	chr15:34430600-34446600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr15:34431000-34446200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:34431000-34446400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:34431200-34439600	Weak transcription	Fetal Brain Female	brain
33	chr15:34431200-34445600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:34431200-34446400	Weak transcription	K562	blood
35	chr15:34431200-34453200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr15:34431400-34446000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:34431400-34446800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:34431600-34439600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:34431600-34442600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr15:34432000-34440400	Weak transcription	Small Intestine	intestine
41	chr15:34432000-34446400	Weak transcription	Brain Substantia Nigra	brain
42	chr15:34432800-34446400	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr15:34433000-34446600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr15:34433000-34446800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr15:34433200-34441800	Weak transcription	Pancreas	Pancrea
46	chr15:34433200-34442800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr15:34433200-34448200	Weak transcription	Gastric	stomach
48	chr15:34433400-34443400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr15:34433400-34446400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr15:34433400-34453200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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