Variant report

Variant	rs16971726
Chromosome Location	chr15:41558037-41558038
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	chr15:41554916..41558076-chr15:41560482..41563886,4	K562	blood:
2	chr15:41548726..41552355-chr15:41557074..41560902,3	K562	blood:

Variant related genes	Relation type
ENSG00000187446	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 20 )

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

rs_ID	r²[population]
rs10518717	1.00[CHB][hapmap]
rs11070328	1.00[CHB][hapmap]
rs11630656	1.00[CHB][hapmap]
rs11854081	1.00[CHB][hapmap]
rs11854632	1.00[CHB][hapmap]
rs11855906	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11856169	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858812	1.00[CHB][hapmap]
rs13313520	1.00[CHB][hapmap]
rs1757468	1.00[CHB][hapmap]
rs17730589	1.00[CHB][hapmap]
rs17730888	1.00[CHB][hapmap]
rs1899	1.00[CHB][hapmap]
rs2118740	1.00[CHB][hapmap]
rs2730056	1.00[CHB][hapmap]
rs28374715	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463309	1.00[CHB][hapmap]
rs28493702	1.00[CHB][hapmap];0.80[MEX][hapmap]
rs28554139	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28557159	1.00[CHB][hapmap]
rs28671712	0.84[EUR][1000 genomes]
rs316611	1.00[CHB][hapmap]
rs3204853	1.00[CHB][hapmap]
rs513280	1.00[CHB][hapmap]
rs522063	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs7164211	1.00[CHB][hapmap]
rs7164684	1.00[CHB][hapmap]
rs7165914	1.00[CHB][hapmap]
rs7168307	1.00[CHB][hapmap]
rs7168431	1.00[CHB][hapmap]
rs7169543	1.00[CHB][hapmap]
rs7181982	1.00[CHB][hapmap]
rs72737786	0.86[AMR][1000 genomes]
rs72737792	0.88[AMR][1000 genomes]
rs72737793	0.88[AMR][1000 genomes]
rs72739609	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023530	1.00[CHB][hapmap]
rs8036026	1.00[CHB][hapmap]
rs8037574	1.00[CHB][hapmap]
rs8043237	0.88[AMR][1000 genomes]
rs9568	1.00[CHB][hapmap]

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	nsv1045455	chr15:41536624-41620534	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs16971726	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs16971726	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs16971726	NDUFAF1	cis	parietal	SCAN
rs16971726	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs16971726	NDUFAF1	cis	cerebellum	SCAN
rs16971726	NUSAP1	cis	cerebellum	SCAN
rs16971726	GPR176	cis	parietal	SCAN
rs16971726	OIP5-AS1	cis	Artery Tibial	GTEx
rs16971726	NDUFAF1	cis	Muscle Skeletal	GTEx
rs16971726	NDUFAF1	cis	lung	GTEx
rs16971726	BUB1B	cis	parietal	SCAN
rs16971726	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs16971726	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs16971726	NDUFAF1	cis	multi-tissue	Pritchard
rs16971726	NDUFAF1	cis	Thyroid	GTEx
rs16971726	NUSAP1	cis	parietal	SCAN
rs16971726	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs16971726	NDUFAF1	cis	lymphoblastoid	seeQTL
rs16971726	NDUFAF1	cis	Whole Blood	GTEx
rs16971726	GPR176	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41524200-41563800	Weak transcription	Small Intestine	intestine
2	chr15:41524200-41575800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:41524800-41563800	Weak transcription	Esophagus	oesophagus
4	chr15:41525200-41575400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:41525800-41575200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr15:41536600-41573600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:41537400-41570800	Weak transcription	Ovary	ovary
8	chr15:41537600-41562800	Weak transcription	Lung	lung
9	chr15:41542800-41572000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr15:41543000-41575200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:41545000-41571400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:41549200-41575200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:41550400-41571400	Weak transcription	Right Ventricle	heart
14	chr15:41550400-41575600	Weak transcription	Fetal Brain Male	brain
15	chr15:41550600-41564200	Weak transcription	NHDF-Ad	bronchial
16	chr15:41551800-41568600	Weak transcription	Fetal Lung	lung
17	chr15:41551800-41570600	Weak transcription	HMEC	breast
18	chr15:41552400-41574600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:41552600-41575200	Weak transcription	GM12878-XiMat	blood
20	chr15:41552800-41575800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr15:41553000-41560000	Strong transcription	Fetal Intestine Small	intestine
22	chr15:41553600-41569200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:41554400-41559600	Strong transcription	Fetal Muscle Trunk	muscle
24	chr15:41554600-41558600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:41554600-41559000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:41554600-41559000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:41554600-41559600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:41554600-41560600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:41554600-41573000	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:41554800-41558400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:41554800-41558600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:41554800-41559000	Strong transcription	Colon Smooth Muscle	Colon
33	chr15:41554800-41559200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr15:41554800-41559600	Strong transcription	Fetal Intestine Large	intestine
35	chr15:41554800-41563400	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:41555000-41558200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:41555000-41558400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:41555000-41558400	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr15:41555000-41560200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:41555000-41561400	Strong transcription	Fetal Stomach	stomach
41	chr15:41555400-41569000	Weak transcription	Fetal Kidney	kidney
42	chr15:41555400-41570800	Weak transcription	HSMM	muscle
43	chr15:41555600-41564200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:41555600-41566600	Weak transcription	Brain Angular Gyrus	brain
45	chr15:41555600-41569000	Weak transcription	Dnd41	blood
46	chr15:41555600-41570600	Strong transcription	Liver	Liver
47	chr15:41555800-41558400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:41556200-41569000	Weak transcription	K562	blood
49	chr15:41556400-41558800	Strong transcription	Hela-S3	cervix
50	chr15:41556400-41559600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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