Variant report

Variant	rs11855248
Chromosome Location	chr15:41276158-41276159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41275943-41276536	K562	blood:	n/a	n/a
2	POLR2A	chr15:41276043-41276267	HepG2	liver:	n/a	n/a
3	POLR2A	chr15:41276141-41276178	MCF-7	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:41276147-41276197	GM12891	blood:	n/a
2	chr15:41276147-41276197	RPTEC	kidney:	n/a
3	chr15:41276147-41276197	PrEC	prostate:	n/a
4	chr15:41276147-41276197	HCPEpiC	choroid plexus:	n/a
5	chr15:41276147-41276197	NH-A	brain:	n/a
6	chr15:41276147-41276197	SK-N-MC	brain:	n/a
7	chr15:41276147-41276197	HRE	kidney:	n/a
8	chr15:41276147-41276197	Caco-2	colon:	n/a
9	chr15:41276147-41276197	CMK	blood:	n/a
10	chr15:41276147-41276197	AG09319	gingival:	n/a
11	chr15:41276147-41276197	HCF	heart:	n/a
12	chr15:41276147-41276197	HCT-116	colon:	n/a
13	chr15:41276147-41276197	AG04450	lung:	fetal
14	chr15:41276147-41276197	Jurkat	blood:	n/a
15	chr15:41276147-41276197	AoSMC	blood vessel:	n/a
16	chr15:41276147-41276197	HIPEpiC	eye:	n/a
17	chr15:41276147-41276197	BJ	skin:	n/a
18	chr15:41276147-41276197	GM12878	blood:	n/a
19	chr15:41276147-41276197	HRCEpiC	kidney:	n/a
20	chr15:41276147-41276197	H1-hESC	embryonic stem cell:	embryo
21	chr15:41276147-41276197	Hela-S3	cervix:	n/a
22	chr15:41276147-41276197	PANC-1	pancreas:	n/a
23	chr15:41276147-41276197	PFSK-1	brain:	n/a
24	chr15:41276147-41276197	NT2-D1	testis:	n/a
25	chr15:41276147-41276197	HMEC	breast:	n/a
26	chr15:41276147-41276197	NHDF-neo	bronchial:	n/a
27	chr15:41276147-41276197	SKMC	muscle:	n/a
28	chr15:41276147-41276197	GM06990	blood:	n/a
29	chr15:41276147-41276197	ECC-1	luminal epithelium:	n/a
30	chr15:41276147-41276197	AG10803	skin:	n/a
31	chr15:41276147-41276197	T-47D	breast:	n/a
32	chr15:41276147-41276197	LNCaP	prostate:	n/a
33	chr15:41276147-41276197	MCF10A-Er-Src	breast:	n/a
34	chr15:41276147-41276197	U87	brain:	n/a
35	chr15:41276147-41276197	HEK293	kidney:	embryo
36	chr15:41276147-41276197	HEEpiC	esophagus:	n/a
37	chr15:41276147-41276197	GM19239	blood:	n/a
38	chr15:41276147-41276197	HRPEpiC	eye:	n/a
39	chr15:41276147-41276197	MCF-7	breast:	n/a
40	chr15:41276147-41276197	ovcar-3	ovarian:	n/a
41	chr15:41276147-41276197	HL-60	blood:	n/a
42	chr15:41276147-41276197	BE2_C	brain:	n/a
43	chr15:41276147-41276197	AG09309	skin:	n/a
44	chr15:41276147-41276197	IMR90	lung:	fetal
45	chr15:41276147-41276197	NB4	blood:	n/a
46	chr15:41276147-41276197	HAEpiC	amniotic membrane:	n/a
47	chr15:41276147-41276197	SK-N-SH_RA	brain:	n/a
48	chr15:41276147-41276197	AG04449	skin:	fetal
49	chr15:41276147-41276197	GM12892	blood:	n/a
50	chr15:41276147-41276197	Hepatocyte	liver:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41243575..41247241-chr15:41275161..41277167,3	MCF-7	breast:

No data

Variant related genes	Relation type
INO80	TF binding region
INO80	CpG island
ENSG00000128965	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1001341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1009913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11070314	0.83[EUR][1000 genomes]
rs11070315	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11070317	0.86[EUR][1000 genomes]
rs11854472	0.83[EUR][1000 genomes]
rs11856572	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11856577	0.84[ASN][1000 genomes]
rs11856848	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs11858678	0.82[MEX][hapmap]
rs12593739	0.83[EUR][1000 genomes]
rs12899590	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12905926	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910027	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329511	0.96[ASN][1000 genomes]
rs1678750	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs1869907	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1962410	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1983400	0.80[ASN][1000 genomes]
rs2306083	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2412572	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2412574	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28473405	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28479904	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28501589	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28538500	0.83[EUR][1000 genomes]
rs28572344	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28581803	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2899002	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2925342	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2925343	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2925345	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2925346	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2927061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2927062	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2947493	0.80[ASN][1000 genomes]
rs2947494	0.80[ASN][1000 genomes]
rs3100807	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3101436	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3214068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3900905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3986311	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4244584	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4497658	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs476633	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4923890	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924519	0.82[EUR][1000 genomes]
rs4924520	0.83[EUR][1000 genomes]
rs4924521	0.83[EUR][1000 genomes]
rs4924522	0.82[EUR][1000 genomes]
rs4924523	0.82[EUR][1000 genomes]
rs4924524	0.82[EUR][1000 genomes]
rs4924525	0.85[EUR][1000 genomes]
rs4924526	0.83[EUR][1000 genomes]
rs4924528	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4924532	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60588038	0.83[EUR][1000 genomes]
rs6492978	0.85[ASN][1000 genomes]
rs692153	0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs692155	0.96[CEU][hapmap];0.85[CHB][hapmap]
rs7162992	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169375	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7171437	0.96[ASN][1000 genomes]
rs7179681	0.85[ASN][1000 genomes]
rs7181816	0.83[EUR][1000 genomes]
rs72735675	0.83[EUR][1000 genomes]
rs72737704	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8023345	0.87[ASN][1000 genomes]
rs8030306	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8042088	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9796	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][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	esv1794127	chr15:41245289-41276158	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1053462	chr15:41270067-41396094	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11855248	NDUFAF1	cis	Muscle Skeletal	GTEx
rs11855248	NDUFAF1	cis	parietal	SCAN
rs11855248	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs11855248	NDUFAF1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41258800-41348400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:41266800-41277400	Strong transcription	Fetal Muscle Leg	muscle
3	chr15:41266800-41278400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:41266800-41280200	Strong transcription	Fetal Brain Female	brain
5	chr15:41266800-41280400	Strong transcription	Brain Substantia Nigra	brain
6	chr15:41266800-41281400	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr15:41266800-41283800	Strong transcription	A549	lung
8	chr15:41266800-41290000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:41266800-41298400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:41267000-41280600	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:41267000-41280800	Strong transcription	Brain Germinal Matrix	brain
12	chr15:41267200-41294800	Strong transcription	Primary T cells from cord blood	blood
13	chr15:41267600-41280600	Strong transcription	Fetal Stomach	stomach
14	chr15:41267600-41294200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:41267600-41301200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:41267800-41280600	Strong transcription	Fetal Intestine Large	intestine
17	chr15:41267800-41280800	Strong transcription	Ovary	ovary
18	chr15:41267800-41281000	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr15:41267800-41281000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:41267800-41282000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr15:41267800-41284400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:41267800-41284600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:41267800-41290200	Strong transcription	NHEK	skin
24	chr15:41267800-41290800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:41267800-41294200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:41267800-41301400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr15:41268000-41277800	Strong transcription	Fetal Kidney	kidney
28	chr15:41268000-41278000	Strong transcription	Gastric	stomach
29	chr15:41268000-41279600	Strong transcription	Small Intestine	intestine
30	chr15:41268000-41280000	Strong transcription	Colonic Mucosa	Colon
31	chr15:41268000-41280200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr15:41268000-41280200	Strong transcription	Left Ventricle	heart
33	chr15:41268000-41280400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr15:41268000-41280400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:41268000-41280400	Strong transcription	Brain Anterior Caudate	brain
36	chr15:41268000-41280400	Strong transcription	Brain Cingulate Gyrus	brain
37	chr15:41268000-41280400	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:41268000-41280600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:41268000-41280600	Strong transcription	Colon Smooth Muscle	Colon
40	chr15:41268000-41280800	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr15:41268000-41281600	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr15:41268000-41282200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:41268000-41284000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr15:41268000-41284000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr15:41268000-41284800	Strong transcription	Fetal Intestine Small	intestine
46	chr15:41268000-41285000	Strong transcription	Dnd41	blood
47	chr15:41268000-41290200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:41268000-41292800	Strong transcription	Liver	Liver
49	chr15:41268000-41294800	Strong transcription	Fetal Thymus	thymus
50	chr15:41268000-41298000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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