Variant report

Variant	rs28554139
Chromosome Location	chr15:41531084-41531085
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41529867..41531714-chr15:41575007..41577019,2	K562	blood:
2	chr15:41521136..41528560-chr15:41530721..41537224,13	K562	blood:

Variant related genes	Relation type
ENSG00000247556	Chromatin interaction
ENSG00000178997	Chromatin interaction
ENSG00000187446	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10518717	1.00[CHB][hapmap]
rs10851403	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11070328	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs11630656	1.00[CHB][hapmap]
rs11852419	0.89[EUR][1000 genomes]
rs11854081	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs11854632	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs11855854	0.85[EUR][1000 genomes]
rs11855906	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11856169	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13313520	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs13329235	0.93[EUR][1000 genomes]
rs13329579	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13380007	0.81[YRI][hapmap]
rs16971726	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]
rs17730589	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs17730888	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs1899	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs2118740	1.00[CHB][hapmap]
rs2448402	0.89[EUR][1000 genomes]
rs28374715	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382348	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28463309	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs28493087	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28493702	1.00[CHB][hapmap];0.80[MEX][hapmap];0.87[YRI][hapmap]
rs28524914	0.94[EUR][1000 genomes]
rs28538451	0.89[EUR][1000 genomes]
rs28557159	1.00[CHB][hapmap]
rs28671712	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28827035	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3204853	1.00[CHB][hapmap]
rs513280	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs521890	0.91[EUR][1000 genomes]
rs522063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs533210	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs691011	0.91[EUR][1000 genomes]
rs691629	0.91[EUR][1000 genomes]
rs691906	0.91[EUR][1000 genomes]
rs691907	0.91[EUR][1000 genomes]
rs7164211	1.00[CHB][hapmap];0.87[YRI][hapmap]
rs7164684	1.00[CHB][hapmap]
rs7165914	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs7168307	1.00[CHB][hapmap]
rs7168431	1.00[CHB][hapmap]
rs7169543	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs7181982	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs72737786	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72737792	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72737793	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72739609	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8023530	1.00[CHB][hapmap]
rs8036026	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs8037574	1.00[CHB][hapmap]
rs8038983	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8043237	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9568	1.00[CHB][hapmap]

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	nsv457120	chr15:41410705-41546631	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv569231	chr15:41410705-41546631	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv1844058	chr15:41511916-41548948	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs28554139	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs28554139	NDUFAF1	cis	Muscle Skeletal	GTEx
rs28554139	NDUFAF1	cis	Thyroid	GTEx
rs28554139	GPR176	cis	cerebellum	SCAN
rs28554139	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs28554139	NDUFAF1	cis	parietal	SCAN
rs28554139	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs28554139	GPR176	cis	parietal	SCAN
rs28554139	NDUFAF1	cis	multi-tissue	Pritchard
rs28554139	BUB1B	cis	parietal	SCAN
rs28554139	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs28554139	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs28554139	NUSAP1	cis	cerebellum	SCAN
rs28554139	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs28554139	OIP5-AS1	cis	Artery Tibial	GTEx
rs28554139	NUSAP1	cis	parietal	SCAN
rs28554139	NDUFAF1	cis	Whole Blood	GTEx
rs28554139	NDUFAF1	cis	cerebellum	SCAN
rs28554139	NDUFAF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41524200-41533200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:41524200-41533400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:41524200-41535800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:41524200-41536600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:41524200-41546200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:41524200-41554800	Weak transcription	Fetal Thymus	thymus
7	chr15:41524200-41555800	Weak transcription	Aorta	Aorta
8	chr15:41524200-41563800	Weak transcription	Small Intestine	intestine
9	chr15:41524200-41575800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:41524400-41532400	Weak transcription	Fetal Intestine Small	intestine
11	chr15:41524400-41533400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:41524400-41533600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:41524400-41533600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:41524400-41535800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:41524400-41536600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:41524400-41555800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:41524600-41533400	Weak transcription	Primary B cells from cord blood	blood
18	chr15:41524600-41533600	Weak transcription	Thymus	Thymus
19	chr15:41524600-41536400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:41524600-41536600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:41524800-41533000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr15:41524800-41533200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:41524800-41533400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:41524800-41533600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:41524800-41535800	Weak transcription	Ovary	ovary
26	chr15:41524800-41546200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr15:41524800-41563800	Weak transcription	Esophagus	oesophagus
28	chr15:41525000-41533400	Weak transcription	Primary T cells from cord blood	blood
29	chr15:41525000-41533600	Weak transcription	Placenta	Placenta
30	chr15:41525000-41535400	Weak transcription	Fetal Stomach	stomach
31	chr15:41525000-41548400	Weak transcription	Fetal Lung	lung
32	chr15:41525200-41532600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:41525200-41533400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:41525200-41533400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:41525200-41533400	Weak transcription	Brain Anterior Caudate	brain
36	chr15:41525200-41533600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:41525200-41533600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:41525200-41548200	Weak transcription	Fetal Kidney	kidney
39	chr15:41525200-41554200	Weak transcription	Fetal Brain Female	brain
40	chr15:41525200-41556400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:41525200-41575400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr15:41525400-41532400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr15:41525400-41532400	Weak transcription	Fetal Intestine Large	intestine
44	chr15:41525400-41533200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr15:41525400-41533400	Weak transcription	Brain Hippocampus Middle	brain
46	chr15:41525400-41533400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr15:41525400-41533600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr15:41525400-41533600	Weak transcription	Spleen	Spleen
49	chr15:41525400-41536400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:41525400-41538800	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links