Variant report

Variant	rs6499255
Chromosome Location	chr16:69830328-69830329
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	MYC	chr16:69830321-69830348	MCF-7	breast:	n/a	n/a
3	RAD21	chr16:69830038-69831181	SK-N-SH	brain:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
4	ZMIZ1	chr16:69830262-69830764	K562	blood:	n/a	n/a
5	RAD21	chr16:69830119-69830995	A549	lung:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
6	CTCF	chr16:69830240-69830390	NHEK	skin:	n/a	n/a
7	SP1	chr16:69830033-69830768	A549	lung:	n/a	n/a
8	RAD21	chr16:69830327-69830818	SK-N-SH_RA	brain:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
9	SP4	chr16:69830269-69830832	H1-hESC	embryonic stem cell:	n/a	n/a
10	JUND	chr16:69830262-69830708	H1-hESC	embryonic stem cell:	n/a	n/a
11	EP300	chr16:69830177-69830631	H1-hESC	embryonic stem cell:	n/a	n/a
12	USF1	chr16:69830258-69830657	H1-hESC	embryonic stem cell:	n/a	n/a
13	SMC3	chr16:69830057-69831495	SK-N-SH	brain:	n/a	chr16:69830586-69830600 chr16:69830586-69830594
14	CTCF	chr16:69830259-69830330	GM10248	blood:	n/a	n/a
15	RAD21	chr16:69830325-69830801	ECC-1	luminal epithelium:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
16	WRNIP1	chr16:69830223-69830919	GM12878	blood:	n/a	n/a
17	BHLHE40	chr16:69830296-69830713	K562	blood:	n/a	n/a
18	CTCF	chr16:69830220-69830370	HCFaa	heart:	n/a	n/a
19	SP1	chr16:69830181-69830667	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr16:69830271-69830741	MCF-7	breast:	n/a	chr16:69830589-69830599 chr16:69830584-69830602 chr16:69830587-69830596 chr16:69830586-69830607
21	RAD21	chr16:69830305-69830889	H1-hESC	embryonic stem cell:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
22	RAD21	chr16:69830308-69830843	H1-hESC	embryonic stem cell:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
23	CTCF	chr16:69830298-69830330	GM19240	blood:	n/a	n/a
24	RAD21	chr16:69830271-69830901	ECC-1	luminal epithelium:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
25	CTCF	chr16:69830260-69830410	GM12878	blood:	n/a	n/a
26	CTCF	chr16:69830273-69830349	GM12892	blood:	n/a	n/a
27	SMC3	chr16:69830195-69830957	HepG2	liver:	n/a	chr16:69830586-69830600 chr16:69830586-69830594
28	RAD21	chr16:69830211-69830931	HCT-116	colon:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
29	CTCF	chr16:69830251-69830397	MCF-7	breast:	n/a	n/a
30	CTCF	chr16:69830311-69830804	HCT-116	colon:	n/a	chr16:69830589-69830599 chr16:69830584-69830602 chr16:69830587-69830596 chr16:69830586-69830607
31	CTCF	chr16:69830223-69830364	GM19239	blood:	n/a	n/a
32	CTCF	chr16:69830259-69830857	HCT-116	colon:	n/a	chr16:69830589-69830599 chr16:69830584-69830602 chr16:69830587-69830596 chr16:69830586-69830607
33	RAD21	chr16:69830295-69831026	HepG2	liver:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
34	CTCF	chr16:69829934-69831562	SK-N-SH	brain:	n/a	chr16:69830589-69830599 chr16:69830584-69830602 chr16:69831014-69831023 chr16:69830587-69830596 chr16:69830586-69830607
35	USF1	chr16:69830243-69830552	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr16:69830295-69830335	GM19238	blood:	n/a	n/a
37	BRCA1	chr16:69830215-69830756	H1-hESC	embryonic stem cell:	n/a	n/a
38	RAD21	chr16:69830261-69830846	HCT-116	colon:	n/a	chr16:69830586-69830595 chr16:69830585-69830604
39	CTCF	chr16:69830240-69830328	GM12878	blood:	n/a	n/a
40	EP300	chr16:69830112-69830734	H1-hESC	embryonic stem cell:	n/a	n/a
41	CHD1	chr16:69830229-69830693	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr16:69830320-69830470	SAEC	small airway:	n/a	n/a
43	CTCF	chr16:69829879-69831279	A549	lung:	n/a	chr16:69830589-69830599 chr16:69830584-69830602 chr16:69831014-69831023 chr16:69830587-69830596 chr16:69830586-69830607
44	SP1	chr16:69830129-69830729	A549	lung:	n/a	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
ENSG00000252443	Chromatin interaction
ENSG00000198373	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10454066	1.00[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap]
rs10500551	1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs10852458	1.00[CEU][hapmap]
rs11075730	0.82[MEX][hapmap]
rs11075733	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11075734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11075738	0.92[AFR][1000 genomes]
rs1139178	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11639947	1.00[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs11641233	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap]
rs11641521	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11643926	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11644838	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11644914	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12232410	0.95[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs12446201	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12447326	0.82[MEX][hapmap]
rs12595869	1.00[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs12596679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12596823	1.00[CEU][hapmap]
rs12925371	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1437135	1.00[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap]
rs16959025	1.00[CEU][hapmap]
rs1800566	1.00[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs2361838	1.00[CEU][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs3169315	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap]
rs3743673	1.00[CEU][hapmap]
rs3811349	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4078387	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4275849	0.88[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs4464069	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4497676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4580150	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4608327	0.92[YRI][hapmap]
rs4985518	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55863174	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55992518	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56282083	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57518557	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60231938	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61426398	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6499253	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7189424	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7193221	0.88[ASW][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs7198242	1.00[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs73579458	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73579497	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8045682	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8046314	1.00[CEU][hapmap]
rs8059345	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8063219	0.88[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs9788837	1.00[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs9921045	1.00[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]

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	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
2	nsv528905	chr16:69829875-69830328	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
IgE levels	23146381	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6499255	FAM96B	cis	parietal	SCAN
rs6499255	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs6499255	SLC7A6	cis	cerebellum	SCAN
rs6499255	HPR	cis	cerebellum	SCAN

Chromatin state (count:125 , 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	chr16:69822800-69830400	Weak transcription	Fetal Muscle Leg	muscle
23	chr16:69822800-69832600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr16:69823000-69832600	Weak transcription	Colonic Mucosa	Colon
25	chr16:69823400-69832400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr16:69823800-69830400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr16:69823800-69832600	Weak transcription	Esophagus	oesophagus
28	chr16:69823800-69832600	Weak transcription	Placenta	Placenta
29	chr16:69823800-69874800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr16:69824000-69830600	Weak transcription	Aorta	Aorta
31	chr16:69824000-69832600	Weak transcription	Left Ventricle	heart
32	chr16:69824000-69833000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr16:69824000-69833000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr16:69824000-69833200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr16:69824200-69830400	Weak transcription	Lung	lung
36	chr16:69824200-69832600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr16:69824200-69833000	Weak transcription	Spleen	Spleen
38	chr16:69824200-69852400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr16:69824400-69833000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr16:69824600-69832400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr16:69824600-69832600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr16:69824600-69832600	Weak transcription	Gastric	stomach
43	chr16:69824800-69830400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr16:69826200-69832000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr16:69826800-69832000	Weak transcription	Primary B cells from cord blood	blood
46	chr16:69826800-69832400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr16:69826800-69832800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr16:69827000-69831000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr16:69827000-69832600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr16:69827000-69832600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links