Variant report

Variant	rs60231938
Chromosome Location	chr16:69830415-69830416
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr16:69830242-69830861	HepG2	liver:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
2	CTCF	chr16:69830380-69830530	WI-38	lung:	n/a	n/a
3	BCLAF1	chr16:69830355-69830832	GM12878	blood:	n/a	n/a
4	RAD21	chr16:69830390-69830841	HepG2	liver:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
5	RAD21	chr16:69830038-69831181	SK-N-SH	brain:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
6	MYC	chr16:69830400-69830443	HUVEC	blood vessel:	n/a	n/a
7	CTCF	chr16:69830377-69830823	K562	blood:	n/a	chr16:69830589-69830599 chr16:69830584-69830602 chr16:69830587-69830596 chr16:69830586-69830607
8	ZMIZ1	chr16:69830262-69830764	K562	blood:	n/a	n/a
9	RAD21	chr16:69830119-69830995	A549	lung:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
10	CTCF	chr16:69830364-69830781	H1-hESC	embryonic stem cell:	n/a	chr16:69830589-69830599 chr16:69830584-69830602 chr16:69830587-69830596 chr16:69830586-69830607
11	CTCF	chr16:69830407-69830779	A549	lung:	n/a	chr16:69830589-69830599 chr16:69830584-69830602 chr16:69830587-69830596 chr16:69830586-69830607
12	RAD21	chr16:69830400-69830837	Hela-S3	cervix:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
13	SP1	chr16:69830033-69830768	A549	lung:	n/a	n/a
14	CTCF	chr16:69830337-69830807	A549	lung:	n/a	chr16:69830589-69830599 chr16:69830584-69830602 chr16:69830587-69830596 chr16:69830586-69830607
15	RAD21	chr16:69830391-69830825	GM12878	blood:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
16	RCOR1	chr16:69830343-69830767	HepG2	liver:	n/a	n/a
17	MYC	chr16:69830348-69830425	MCF-7	breast:	n/a	n/a
18	POU2F2	chr16:69830337-69830775	GM12878	blood:	n/a	n/a
19	RAD21	chr16:69830327-69830818	SK-N-SH_RA	brain:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
20	SP4	chr16:69830269-69830832	H1-hESC	embryonic stem cell:	n/a	n/a
21	JUND	chr16:69830262-69830708	H1-hESC	embryonic stem cell:	n/a	n/a
22	EP300	chr16:69830177-69830631	H1-hESC	embryonic stem cell:	n/a	n/a
23	MYC	chr16:69830352-69830718	H1-hESC	embryonic stem cell:	n/a	n/a
24	USF1	chr16:69830258-69830657	H1-hESC	embryonic stem cell:	n/a	n/a
25	SMC3	chr16:69830057-69831495	SK-N-SH	brain:	n/a	chr16:69830586-69830600 chr16:69830586-69830594
26	RAD21	chr16:69830325-69830801	ECC-1	luminal epithelium:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
27	WRNIP1	chr16:69830223-69830919	GM12878	blood:	n/a	n/a
28	BHLHE40	chr16:69830296-69830713	K562	blood:	n/a	n/a
29	SMC3	chr16:69830337-69830945	K562	blood:	n/a	chr16:69830586-69830600 chr16:69830586-69830594
30	GTF2F1	chr16:69830358-69830696	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr16:69830368-69830796	H1-hESC	embryonic stem cell:	n/a	n/a
32	SP1	chr16:69830181-69830667	H1-hESC	embryonic stem cell:	n/a	n/a
33	RAD21	chr16:69830376-69830783	SK-N-SH_RA	brain:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
34	CTCF	chr16:69830271-69830741	MCF-7	breast:	n/a	chr16:69830589-69830599 chr16:69830584-69830602 chr16:69830587-69830596 chr16:69830586-69830607
35	RAD21	chr16:69830348-69830914	A549	lung:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
36	RAD21	chr16:69830305-69830889	H1-hESC	embryonic stem cell:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
37	CTCF	chr16:69830343-69830839	HepG2	liver:	n/a	chr16:69830589-69830599 chr16:69830584-69830602 chr16:69830587-69830596 chr16:69830586-69830607
38	CTCF	chr16:69830397-69830955	K562	blood:	n/a	chr16:69830589-69830599 chr16:69830584-69830602 chr16:69830587-69830596 chr16:69830586-69830607
39	RAD21	chr16:69830308-69830843	H1-hESC	embryonic stem cell:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
40	SMC3	chr16:69830403-69830821	GM12878	blood:	n/a	chr16:69830586-69830600 chr16:69830586-69830594
41	RAD21	chr16:69830271-69830901	ECC-1	luminal epithelium:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
42	RAD21	chr16:69830380-69830838	H1-hESC	embryonic stem cell:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
43	HDAC2	chr16:69830415-69830792	HepG2	liver:	n/a	n/a
44	SMC3	chr16:69830195-69830957	HepG2	liver:	n/a	chr16:69830586-69830600 chr16:69830586-69830594
45	RAD21	chr16:69830211-69830931	HCT-116	colon:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
46	CTCF	chr16:69830311-69830804	HCT-116	colon:	n/a	chr16:69830589-69830599 chr16:69830584-69830602 chr16:69830587-69830596 chr16:69830586-69830607
47	CTCF	chr16:69830259-69830857	HCT-116	colon:	n/a	chr16:69830589-69830599 chr16:69830584-69830602 chr16:69830587-69830596 chr16:69830586-69830607
48	RAD21	chr16:69830295-69831026	HepG2	liver:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
49	CTCF	chr16:69830371-69830820	IMR90	lung:	n/a	chr16:69830589-69830599 chr16:69830584-69830602 chr16:69830587-69830596 chr16:69830586-69830607
50	JUND	chr16:69830404-69830740	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:69830414-69830464	BE2_C	brain:	n/a
2	chr16:69830414-69830464	NHBE	bronchial:	n/a
3	chr16:69830414-69830464	HPAEpiC	pulmonary alveolar:	n/a
4	chr16:69830414-69830464	CMK	blood:	n/a
5	chr16:69830414-69830464	HIPEpiC	eye:	n/a
6	chr16:69830414-69830464	ProgFib	skin:	n/a
7	chr16:69830414-69830464	HCM	heart:	n/a
8	chr16:69830414-69830464	MCF10A-Er-Src	breast:	n/a
9	chr16:69830414-69830464	GM06990	blood:	n/a
10	chr16:69830414-69830464	Hepatocyte	liver:	n/a
11	chr16:69830414-69830464	GM19239	blood:	n/a
12	chr16:69830414-69830464	H1-hESC	embryonic stem cell:	embryo
13	chr16:69830414-69830464	K562	blood:	n/a
14	chr16:69830414-69830464	MCF-7	breast:	n/a
15	chr16:69830414-69830464	HEK293	kidney:	embryo
16	chr16:69830414-69830464	HCT-116	colon:	n/a
17	chr16:69830414-69830464	Hela-S3	cervix:	n/a
18	chr16:69830414-69830464	SAEC	small airway:	n/a
19	chr16:69830414-69830464	PFSK-1	brain:	n/a
20	chr16:69830414-69830464	PrEC	prostate:	n/a
21	chr16:69830414-69830464	AG09319	gingival:	n/a
22	chr16:69830414-69830464	HNPCEpiC	eye:	n/a
23	chr16:69830414-69830464	AG10803	skin:	n/a
24	chr16:69830414-69830464	HRPEpiC	eye:	n/a
25	chr16:69830414-69830464	SK-N-MC	brain:	n/a
26	chr16:69830414-69830464	GM12891	blood:	n/a
27	chr16:69830414-69830464	HRCEpiC	kidney:	n/a
28	chr16:69830414-69830464	SK-N-SH_RA	brain:	n/a
29	chr16:69830414-69830464	NH-A	brain:	n/a
30	chr16:69830414-69830464	ovcar-3	ovarian:	n/a
31	chr16:69830414-69830464	AG04449	skin:	fetal
32	chr16:69830414-69830464	HepG2	liver:	n/a
33	chr16:69830414-69830464	SKMC	muscle:	n/a
34	chr16:69830414-69830464	HCF	heart:	n/a
35	chr16:69830414-69830464	HL-60	blood:	n/a
36	chr16:69830414-69830464	SK-N-SH	brain:	n/a
37	chr16:69830414-69830464	GM12892	blood:	n/a
38	chr16:69830414-69830464	IMR90	lung:	fetal
39	chr16:69830414-69830464	LNCaP	prostate:	n/a
40	chr16:69830414-69830464	HCPEpiC	choroid plexus:	n/a
41	chr16:69830414-69830464	BJ	skin:	n/a
42	chr16:69830414-69830464	NHDF-neo	bronchial:	n/a
43	chr16:69830414-69830464	AG04450	lung:	fetal
44	chr16:69830414-69830464	HEEpiC	esophagus:	n/a
45	chr16:69830414-69830464	NT2-D1	testis:	n/a
46	chr16:69830414-69830464	GM12878	blood:	n/a
47	chr16:69830414-69830464	ECC-1	luminal epithelium:	n/a
48	chr16:69830414-69830464	PANC-1	pancreas:	n/a
49	chr16:69830414-69830464	T-47D	breast:	n/a
50	chr16:69830414-69830464	NB4	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:69830118..69831108-chr16:69893111..69894248,7	MCF-7	breast:
2	chr16:69730776..69732445-chr16:69829537..69832093,2	K562	blood:
3	chr16:69830098..69830907-chr16:69893613..69894173,2	MCF-7	breast:
4	chr16:69830100..69831154-chr16:69963741..69964711,6	K562	blood:
5	chr16:69818416..69821384-chr16:69829195..69831869,2	K562	blood:
6	chr16:69830266..69831089-chr16:69963742..69964770,3	MCF-7	breast:

Variant related genes	Relation type
WWP2	TF binding region
WWP2	CpG island
ENSG00000252443	Chromatin interaction
ENSG00000198373	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11075733	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11075734	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1139178	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11641521	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11643926	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11644838	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11644914	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12446201	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12596679	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12925371	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1437135	0.81[EUR][1000 genomes]
rs2196574	0.81[EUR][1000 genomes]
rs3811349	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4078387	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4341733	0.95[AFR][1000 genomes]
rs4464069	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4497676	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4580150	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4985518	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985523	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55701476	0.82[EUR][1000 genomes]
rs55863174	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55992518	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56282083	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57518557	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59295369	0.81[EUR][1000 genomes]
rs60941540	0.87[AFR][1000 genomes]
rs61426398	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6499253	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6499255	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499257	0.94[AFR][1000 genomes]
rs689455	0.81[EUR][1000 genomes]
rs7186002	0.81[EUR][1000 genomes]
rs7189424	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73579458	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73579497	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8045682	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8059345	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60231938	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69797600-69853400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr16:69806800-69833000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr16:69807000-69832000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr16:69807200-69832600	Weak transcription	NHLF	lung
5	chr16:69807200-69832800	Weak transcription	Pancreas	Pancrea
6	chr16:69807200-69852400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:69807200-69852800	Weak transcription	Hela-S3	cervix
8	chr16:69807200-69854800	Weak transcription	Psoas Muscle	Psoas
9	chr16:69808000-69833200	Weak transcription	HSMM	muscle
10	chr16:69810000-69839800	Weak transcription	HUVEC	blood vessel
11	chr16:69810200-69831000	Weak transcription	NHEK	skin
12	chr16:69810200-69833400	Weak transcription	Dnd41	blood
13	chr16:69815200-69833400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr16:69817800-69854600	Weak transcription	HMEC	breast
15	chr16:69820200-69845000	Weak transcription	K562	blood
16	chr16:69822200-69833000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr16:69822400-69832600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr16:69822400-69833000	Weak transcription	HSMMtube	muscle
19	chr16:69822400-69854800	Weak transcription	Stomach Mucosa	stomach
20	chr16:69822600-69833000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr16:69822600-69833200	Weak transcription	Small Intestine	intestine
22	chr16:69822800-69832600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr16:69823000-69832600	Weak transcription	Colonic Mucosa	Colon
24	chr16:69823400-69832400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr16:69823800-69832600	Weak transcription	Esophagus	oesophagus
26	chr16:69823800-69832600	Weak transcription	Placenta	Placenta
27	chr16:69823800-69874800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr16:69824000-69830600	Weak transcription	Aorta	Aorta
29	chr16:69824000-69832600	Weak transcription	Left Ventricle	heart
30	chr16:69824000-69833000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr16:69824000-69833000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr16:69824000-69833200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr16:69824200-69832600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr16:69824200-69833000	Weak transcription	Spleen	Spleen
35	chr16:69824200-69852400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr16:69824400-69833000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr16:69824600-69832400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr16:69824600-69832600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr16:69824600-69832600	Weak transcription	Gastric	stomach
40	chr16:69826200-69832000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr16:69826800-69832000	Weak transcription	Primary B cells from cord blood	blood
42	chr16:69826800-69832400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr16:69826800-69832800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr16:69827000-69831000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr16:69827000-69832600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr16:69827000-69832600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr16:69827000-69832600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr16:69827000-69832600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr16:69827000-69832600	Weak transcription	Fetal Thymus	thymus
50	chr16:69827000-69832600	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links