Variant report

Variant	rs28631111
Chromosome Location	chr15:41777898-41777899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41773035..41782898-chr15:41783132..41789747,15	K562	blood:
2	chr15:41777763..41779575-chr15:41786284..41787961,2	MCF-7	breast:
3	chr15:41777253..41780203-chr15:41850412..41852434,2	K562	blood:
4	chr15:41768860..41771518-chr15:41776158..41779055,4	K562	blood:

Variant related genes	Relation type
ENSG00000137825	Chromatin interaction
ENSG00000137815	Chromatin interaction
ENSG00000092445	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10518717	1.00[CHB][hapmap]
rs11070328	1.00[CHB][hapmap]
rs11635906	1.00[CHB][hapmap]
rs11854081	1.00[CHB][hapmap]
rs11854632	1.00[CHB][hapmap]
rs11858812	1.00[CHB][hapmap]
rs13313520	1.00[CHB][hapmap]
rs170296	1.00[LWK][hapmap]
rs1757457	1.00[LWK][hapmap]
rs1757468	1.00[CHB][hapmap]
rs17730589	1.00[CHB][hapmap]
rs17730888	1.00[CHB][hapmap]
rs1899	1.00[CHB][hapmap]
rs2730056	1.00[CHB][hapmap];1.00[LWK][hapmap]
rs28463309	1.00[CHB][hapmap]
rs28479336	1.00[ASN][1000 genomes]
rs28503916	1.00[ASN][1000 genomes]
rs28508151	1.00[ASN][1000 genomes]
rs28557159	1.00[CHB][hapmap]
rs28662502	1.00[ASN][1000 genomes]
rs316606	1.00[CHB][hapmap]
rs316607	1.00[CHB][hapmap]
rs316611	1.00[CHB][hapmap];1.00[LWK][hapmap]
rs3204853	1.00[CHB][hapmap]
rs34040639	1.00[CHB][hapmap]
rs4924549	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7164211	1.00[CHB][hapmap]
rs7164684	1.00[CHB][hapmap];1.00[LWK][hapmap]
rs7165914	1.00[CHB][hapmap]
rs7168307	1.00[CHB][hapmap]
rs7168431	1.00[CHB][hapmap];1.00[LWK][hapmap]
rs7169543	1.00[CHB][hapmap]
rs7181982	1.00[CHB][hapmap]
rs72739663	0.89[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]

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	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv904110	chr15:41776692-41813279	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv904111	chr15:41777898-41805115	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28631111	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs28631111	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs28631111	NDUFAF1	cis	lymphoblastoid	seeQTL
rs28631111	NDUFAF1	cis	Muscle Skeletal	GTEx
rs28631111	C15orf57	cis	Artery Tibial	GTEx
rs28631111	NDUFAF1	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41765600-41778400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:41769600-41779200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:41769600-41780200	Weak transcription	Right Atrium	heart
4	chr15:41771600-41780200	Weak transcription	Fetal Heart	heart
5	chr15:41773000-41779600	Weak transcription	HUVEC	blood vessel
6	chr15:41773200-41779200	Weak transcription	Hela-S3	cervix
7	chr15:41773400-41779600	Weak transcription	Colonic Mucosa	Colon
8	chr15:41773400-41785000	Weak transcription	A549	lung
9	chr15:41773600-41778200	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:41773800-41778600	Weak transcription	Aorta	Aorta
11	chr15:41773800-41780000	Weak transcription	HMEC	breast
12	chr15:41773800-41780200	Weak transcription	NHLF	lung
13	chr15:41773800-41784000	Weak transcription	HepG2	liver
14	chr15:41774000-41778800	Weak transcription	Spleen	Spleen
15	chr15:41774000-41779000	Weak transcription	Right Ventricle	heart
16	chr15:41774000-41779400	Weak transcription	Lung	lung
17	chr15:41774000-41782200	Weak transcription	Osteobl	bone
18	chr15:41774600-41779600	Weak transcription	NH-A	brain
19	chr15:41774800-41778000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:41774800-41784600	Weak transcription	Dnd41	blood
21	chr15:41775000-41779400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr15:41775000-41780400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:41775400-41778400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:41775400-41779000	Weak transcription	Adipose Nuclei	Adipose
25	chr15:41775400-41779600	Weak transcription	Fetal Kidney	kidney
26	chr15:41775400-41780000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:41775400-41780000	Weak transcription	Esophagus	oesophagus
28	chr15:41775400-41780000	Weak transcription	Fetal Thymus	thymus
29	chr15:41775400-41780400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr15:41775400-41784800	Weak transcription	Liver	Liver
31	chr15:41775600-41778200	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:41775600-41780000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr15:41775600-41781800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:41775600-41781800	Weak transcription	NHDF-Ad	bronchial
35	chr15:41775600-41782200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:41775600-41783800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr15:41775600-41784800	Weak transcription	Brain Angular Gyrus	brain
38	chr15:41775800-41778000	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:41775800-41778600	Weak transcription	Primary T cells from cord blood	blood
40	chr15:41775800-41778800	Weak transcription	Brain Anterior Caudate	brain
41	chr15:41775800-41780200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr15:41775800-41782200	Weak transcription	HSMMtube	muscle
43	chr15:41776000-41778800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:41776000-41779000	Weak transcription	Brain Substantia Nigra	brain
45	chr15:41776000-41779400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr15:41776000-41779600	Weak transcription	Gastric	stomach
47	chr15:41776000-41779800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:41776000-41780000	Weak transcription	Fetal Lung	lung
49	chr15:41776000-41780000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr15:41776000-41780000	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links