Variant report

Variant	rs7548516
Chromosome Location	chr1:150980281-150980282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr1:150980180-150981912	MCF-7	breast:	n/a	n/a
2	POLR2A	chr1:150980177-150980340	HepG2	liver:	n/a	n/a
3	EP300	chr1:150980106-150981033	HepG2	liver:	n/a	n/a
4	HCFC1	chr1:150980019-150982095	Hela-S3	cervix:	n/a	n/a
5	GABPA	chr1:150980256-150981937	MCF-7	breast:	n/a	n/a
6	SIN3AK20	chr1:150978184-150981996	MCF-7	breast:	n/a	n/a
7	MXI1	chr1:150980226-150982457	IMR90	lung:	n/a	n/a
8	RCOR1	chr1:150980260-150981252	K562	blood:	n/a	n/a
9	POLR2A	chr1:150978695-150981793	HepG2	liver:	n/a	n/a
10	GATA3	chr1:150980271-150981731	MCF-7	breast:	n/a	chr1:150981621-150981631 chr1:150980550-150980559
11	RFX5	chr1:150980095-150981711	SK-N-SH	brain:	n/a	chr1:150980769-150980784 chr1:150980773-150980782 chr1:150980770-150980784
12	NR2F2	chr1:150980068-150982240	K562	blood:	n/a	n/a
13	POLR2A	chr1:150980215-150981663	HUVEC	blood vessel:	n/a	n/a
14	NR2F2	chr1:150979974-150982036	MCF-7	breast:	n/a	n/a
15	MYBL2	chr1:150980279-150981454	HepG2	liver:	n/a	n/a
16	MAX	chr1:150980175-150980300	HepG2	liver:	n/a	n/a
17	CHD1	chr1:150980164-150982412	IMR90	lung:	n/a	chr1:150981521-150981531
18	FOXA1	chr1:150980272-150981020	HepG2	liver:	n/a	n/a
19	TEAD4	chr1:150980207-150982058	K562	blood:	n/a	n/a

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150945812..150948969-chr1:150979293..150982183,4	K562	blood:
2	chr1:150974834..150982774-chr1:151014282..151023779,19	MCF-7	breast:
3	chr1:150849097..150850809-chr1:150979255..150981896,2	MCF-7	breast:
4	chr1:150550535..150554049-chr1:150976755..150981799,6	K562	blood:
5	chr1:150979021..150981360-chr1:151118629..151120745,2	K562	blood:
6	chr1:150532436..150535638-chr1:150978193..150982152,3	MCF-7	breast:
7	chr1:150979291..150984938-chr1:151030285..151033653,10	K562	blood:
8	chr1:150979986..150982538-chr1:151136841..151139170,3	K562	blood:
9	chr1:150953956..150954910-chr1:150980206..150980789,4	MCF-7	breast:
10	chr1:150979099..150980863-chr1:151170963..151172486,2	MCF-7	breast:
11	chr1:150944222..150949507-chr1:150975860..150982521,8	K562	blood:
12	chr1:150977224..150980859-chr1:151016149..151020552,4	K562	blood:
13	chr1:150954014..150954910-chr1:150980209..150980838,4	MCF-7	breast:
14	chr1:150334947..150337371-chr1:150979446..150982037,2	K562	blood:
15	chr1:150951620..150955085-chr1:150979651..150983018,4	K562	blood:
16	chr1:150979416..150982558-chr1:151006468..151010604,5	MCF-7	breast:
17	chr1:150942078..150949693-chr1:150976791..150984782,24	MCF-7	breast:
18	chr1:150952182..150958148-chr1:150976816..150982947,12	MCF-7	breast:
19	chr1:150978624..150980808-chr1:151042705..151044650,2	MCF-7	breast:
20	chr1:150978947..150982308-chr1:151041500..151045951,4	K562	blood:
21	chr1:150977392..150983338-chr1:151040807..151046211,16	MCF-7	breast:
22	chr1:150979239..150982026-chr1:151136822..151140051,3	MCF-7	breast:
23	chr1:150976723..150987587-chr1:151024685..151036322,24	MCF-7	breast:
24	chr1:150979106..150980954-chr1:151030690..151033653,4	K562	blood:
25	chr1:150939149..150940667-chr1:150979140..150981857,2	MCF-7	breast:
26	chr1:150979769..150983967-chr1:151018069..151024059,8	MCF-7	breast:
27	chr1:150979682..150982247-chr1:150996495..150999456,2	MCF-7	breast:

No data

Variant related genes	Relation type
FAM63A	TF binding region
PRUNE	TF binding region
ENSG00000203804	Chromatin interaction
ENSG00000143434	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000231073	Chromatin interaction
ENSG00000143443	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000163141	Chromatin interaction
ENSG00000143412	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143437	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10888397	0.91[CHB][hapmap]
rs10888398	0.86[CHB][hapmap]
rs11579736	0.86[ASN][1000 genomes]
rs11581757	0.91[CHB][hapmap]
rs11583707	0.88[ASN][1000 genomes]
rs12067685	0.88[ASN][1000 genomes]
rs12119409	0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs12141871	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs12145224	0.86[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12405726	0.90[ASN][1000 genomes]
rs12562939	0.88[ASN][1000 genomes]
rs1889741	0.82[CHB][hapmap]
rs2124952	0.91[CHB][hapmap]
rs2272214	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs2280627	0.86[CHB][hapmap]
rs3738478	0.81[CHD][hapmap]
rs4451553	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs4970987	0.91[CHB][hapmap];0.91[YRI][hapmap];0.88[ASN][1000 genomes]
rs4970988	0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[YRI][hapmap];0.87[ASN][1000 genomes]
rs6664622	0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6677420	0.80[ASN][1000 genomes]
rs7518156	0.81[ASN][1000 genomes]
rs752376	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs7556661	0.91[CHB][hapmap]
rs8444	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs897815	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7548516	HORMAD1	cis	Esophagus Mucosa	GTEx
rs7548516	RP11-316M1.12	cis	Whole Blood	GTEx
rs7548516	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs7548516	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs7548516	HORMAD1	cis	normal skin	skin_eQTL
rs7548516	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs7548516	RP11-316M1.12	cis	Thyroid	GTEx
rs7548516	HORMAD1	cis	Nerve Tibial	GTEx
rs7548516	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs7548516	HORMAD1	cis	lesional skin	skin_eQTL
rs7548516	RP11-316M1.12	cis	lung	GTEx
rs7548516	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs7548516	RP11-316M1.12	cis	Artery Tibial	GTEx
rs7548516	CTSS	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150973600-150980800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr1:150975400-150982400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:150977400-150980600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr1:150977400-150981800	Active TSS	Esophagus	oesophagus
5	chr1:150978000-150980800	Flanking Active TSS	Dnd41	blood
6	chr1:150978000-150980800	Flanking Active TSS	K562	blood
7	chr1:150978000-150981400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr1:150978200-150980600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:150978800-150981800	Active TSS	HSMMtube	muscle
10	chr1:150979200-150980400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:150979200-150980600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr1:150979200-150980800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:150979200-150981000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:150979400-150980400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr1:150979400-150980400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:150979400-150980400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:150979400-150980400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:150979400-150980400	Flanking Active TSS	Colonic Mucosa	Colon
19	chr1:150979400-150980400	Enhancers	Fetal Heart	heart
20	chr1:150979400-150980400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr1:150979400-150980400	Enhancers	Small Intestine	intestine
22	chr1:150979400-150980600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:150979400-150980600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:150979400-150980600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr1:150979400-150980600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr1:150979400-150980800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:150979400-150980800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:150979400-150980800	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr1:150979400-150980800	Flanking Active TSS	Liver	Liver
30	chr1:150979400-150980800	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr1:150979400-150980800	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr1:150979400-150980800	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr1:150979400-150980800	Weak transcription	Gastric	stomach
34	chr1:150979400-150980800	Enhancers	Placenta Amnion	Placenta Amnion
35	chr1:150979400-150980800	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr1:150979400-150980800	Flanking Active TSS	Hela-S3	cervix
37	chr1:150979400-150981000	Weak transcription	Lung	lung
38	chr1:150979400-150981000	Weak transcription	Ovary	ovary
39	chr1:150979400-150981000	Enhancers	Spleen	Spleen
40	chr1:150979600-150980400	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr1:150979600-150980400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:150979600-150980400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr1:150979600-150980400	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr1:150979600-150980400	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr1:150979600-150980400	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:150979600-150980400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr1:150979600-150980400	Enhancers	Primary B cells from peripheral blood	blood
48	chr1:150979600-150980400	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr1:150979600-150980400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:150979600-150980400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links