Variant report

Variant	rs4580154
Chromosome Location	chr16:81818860-81818861
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr16:81818725-81819107	GM12878	blood:	n/a	n/a
2	POLR2A	chr16:81818786-81818873	GM12878	blood:	n/a	n/a
3	PML	chr16:81818766-81819419	GM12878	blood:	n/a	chr16:81819035-81819043
4	POLR2A	chr16:81818532-81820366	GM12891	blood:	n/a	n/a
5	WRNIP1	chr16:81818807-81819019	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:81818852-81818902	Jurkat	blood:	n/a
2	chr16:81818852-81818902	GM12892	blood:	n/a
3	chr16:81818852-81818902	HepG2	liver:	n/a
4	chr16:81818852-81818902	LNCaP	prostate:	n/a
5	chr16:81818852-81818902	HMEC	breast:	n/a
6	chr16:81818852-81818902	U87	brain:	n/a
7	chr16:81818852-81818902	HL-60	blood:	n/a
8	chr16:81818852-81818902	ProgFib	skin:	n/a
9	chr16:81818852-81818902	MCF-7	breast:	n/a
10	chr16:81818852-81818902	PFSK-1	brain:	n/a
11	chr16:81818852-81818902	BE2_C	brain:	n/a
12	chr16:81818852-81818902	HRPEpiC	eye:	n/a
13	chr16:81818852-81818902	ECC-1	luminal epithelium:	n/a
14	chr16:81818852-81818902	Caco-2	colon:	n/a
15	chr16:81818852-81818902	HRCEpiC	kidney:	n/a
16	chr16:81818852-81818902	HEEpiC	esophagus:	n/a
17	chr16:81818852-81818902	NB4	blood:	n/a
18	chr16:81818852-81818902	HAEpiC	amniotic membrane:	n/a
19	chr16:81818852-81818902	NH-A	brain:	n/a
20	chr16:81818852-81818902	Hela-S3	cervix:	n/a
21	chr16:81818852-81818902	AG09319	gingival:	n/a
22	chr16:81818852-81818902	HIPEpiC	eye:	n/a
23	chr16:81818852-81818902	HPAEpiC	pulmonary alveolar:	n/a
24	chr16:81818852-81818902	HUVEC	blood vessel:	n/a
25	chr16:81818852-81818902	T-47D	breast:	n/a
26	chr16:81818852-81818902	AG10803	skin:	n/a
27	chr16:81818852-81818902	AoSMC	blood vessel:	n/a
28	chr16:81818852-81818902	PrEC	prostate:	n/a
29	chr16:81818852-81818902	ovcar-3	ovarian:	n/a
30	chr16:81818852-81818902	SKMC	muscle:	n/a
31	chr16:81818852-81818902	HRE	kidney:	n/a
32	chr16:81818852-81818902	GM12891	blood:	n/a
33	chr16:81818852-81818902	IMR90	lung:	fetal
34	chr16:81818852-81818902	HCT-116	colon:	n/a
35	chr16:81818852-81818902	NT2-D1	testis:	n/a
36	chr16:81818852-81818902	H1-hESC	embryonic stem cell:	embryo
37	chr16:81818852-81818902	Hepatocyte	liver:	n/a
38	chr16:81818852-81818902	GM19239	blood:	n/a
39	chr16:81818852-81818902	CMK	blood:	n/a
40	chr16:81818852-81818902	A549	lung:	n/a
41	chr16:81818852-81818902	PANC-1	pancreas:	n/a
42	chr16:81818852-81818902	NHDF-neo	bronchial:	n/a
43	chr16:81818852-81818902	HCM	heart:	n/a
44	chr16:81818852-81818902	GM06990	blood:	n/a
45	chr16:81818852-81818902	K562	blood:	n/a
46	chr16:81818852-81818902	RPTEC	kidney:	n/a
47	chr16:81818852-81818902	MCF10A-Er-Src	breast:	n/a
48	chr16:81818852-81818902	SAEC	small airway:	n/a
49	chr16:81818852-81818902	HNPCEpiC	eye:	n/a
50	chr16:81818852-81818902	AG04450	lung:	fetal

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:81797999..81801347-chr16:81816788..81819306,3	K562	blood:
2	chr16:81811097..81813033-chr16:81817790..81820555,3	MCF-7	breast:

No data

Variant related genes	Relation type
PLCG2	TF binding region
PLCG2	CpG island
ENSG00000197943	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11642139	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11861147	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11866195	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12934353	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4281705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4354929	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4476174	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480797	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4561462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6564920	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7499585	0.82[AMR][1000 genomes]
rs8045964	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8047206	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052218	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][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	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
2	nsv573365	chr16:81804972-81975892	Strong transcription Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4580154	MLYCD	cis	parietal	SCAN
rs4580154	MBTPS1	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81814400-81831800	Weak transcription	Adipose Nuclei	Adipose
2	chr16:81815200-81830000	Weak transcription	Esophagus	oesophagus
3	chr16:81815400-81830600	Weak transcription	Thymus	Thymus
4	chr16:81816400-81819000	Enhancers	Small Intestine	intestine
5	chr16:81816400-81820200	Enhancers	Pancreas	Pancrea
6	chr16:81816400-81820400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr16:81816800-81822200	Weak transcription	Colonic Mucosa	Colon
8	chr16:81817200-81819000	Enhancers	Left Ventricle	heart
9	chr16:81817400-81822200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr16:81817600-81819600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr16:81817800-81819400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr16:81817800-81824000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
13	chr16:81818000-81819600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr16:81818000-81819800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr16:81818000-81821000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr16:81818000-81823200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr16:81818000-81827800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr16:81818000-81830400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr16:81818000-81845000	Genic enhancers	Primary B cells from peripheral blood	blood
20	chr16:81818200-81819200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr16:81818200-81819200	Weak transcription	Lung	lung
22	chr16:81818200-81819400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr16:81818200-81819600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr16:81818200-81819800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr16:81818200-81819800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr16:81818200-81823800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr16:81818400-81819800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr16:81818400-81826000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr16:81818600-81819600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr16:81818600-81819600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr16:81818600-81819600	Weak transcription	Spleen	Spleen
32	chr16:81818600-81820000	Weak transcription	Liver	Liver
33	chr16:81818600-81820400	Genic enhancers	Primary B cells from cord blood	blood
34	chr16:81818600-81824400	Weak transcription	Colon Smooth Muscle	Colon
35	chr16:81818600-81825400	Weak transcription	Fetal Intestine Small	intestine
36	chr16:81818800-81819000	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr16:81818800-81819000	Enhancers	Gastric	stomach
38	chr16:81818800-81819600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr16:81818800-81819800	Weak transcription	Fetal Kidney	kidney
40	chr16:81818800-81820200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr16:81818800-81820400	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr16:81818800-81820600	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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