Variant report

Variant	rs9921711
Chromosome Location	chr16:30394541-30394542
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:30394135-30394825	K562	blood:	n/a	n/a
2	POLR2A	chr16:30393435-30394582	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr16:30393897-30394542	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr16:30393433-30394708	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:30394532-30394582	GM12878	blood:	n/a
2	chr16:30394532-30394582	HPAEpiC	pulmonary alveolar:	n/a
3	chr16:30394532-30394582	U87	brain:	n/a
4	chr16:30394532-30394582	T-47D	breast:	n/a
5	chr16:30394532-30394582	NHDF-neo	bronchial:	n/a
6	chr16:30394532-30394582	Jurkat	blood:	n/a
7	chr16:30394532-30394582	GM12891	blood:	n/a
8	chr16:30394532-30394582	HepG2	liver:	n/a
9	chr16:30394532-30394582	AG04449	skin:	fetal
10	chr16:30394532-30394582	SK-N-MC	brain:	n/a
11	chr16:30394532-30394582	HNPCEpiC	eye:	n/a
12	chr16:30394532-30394582	AG04450	lung:	fetal
13	chr16:30394532-30394582	ECC-1	luminal epithelium:	n/a
14	chr16:30394532-30394582	NT2-D1	testis:	n/a
15	chr16:30394532-30394582	LNCaP	prostate:	n/a
16	chr16:30394532-30394582	Hepatocyte	liver:	n/a
17	chr16:30394532-30394582	ovcar-3	ovarian:	n/a
18	chr16:30394532-30394582	HL-60	blood:	n/a
19	chr16:30394532-30394582	BE2_C	brain:	n/a
20	chr16:30394532-30394582	HMEC	breast:	n/a
21	chr16:30394532-30394582	HRPEpiC	eye:	n/a
22	chr16:30394532-30394582	MCF-7	breast:	n/a
23	chr16:30394532-30394582	H1-hESC	embryonic stem cell:	embryo
24	chr16:30394532-30394582	GM06990	blood:	n/a
25	chr16:30394532-30394582	HIPEpiC	eye:	n/a
26	chr16:30394532-30394582	RPTEC	kidney:	n/a
27	chr16:30394532-30394582	HCM	heart:	n/a
28	chr16:30394532-30394582	HEEpiC	esophagus:	n/a
29	chr16:30394532-30394582	AG09319	gingival:	n/a
30	chr16:30394532-30394582	SAEC	small airway:	n/a
31	chr16:30394532-30394582	Caco-2	colon:	n/a
32	chr16:30394532-30394582	HRCEpiC	kidney:	n/a
33	chr16:30394532-30394582	CMK	blood:	n/a
34	chr16:30394532-30394582	AG09309	skin:	n/a
35	chr16:30394532-30394582	BJ	skin:	n/a
36	chr16:30394532-30394582	SK-N-SH	brain:	n/a
37	chr16:30394532-30394582	NH-A	brain:	n/a
38	chr16:30394532-30394582	IMR90	lung:	fetal
39	chr16:30394532-30394582	AG10803	skin:	n/a
40	chr16:30394532-30394582	HCPEpiC	choroid plexus:	n/a
41	chr16:30394532-30394582	HEK293	kidney:	embryo
42	chr16:30394532-30394582	HAEpiC	amniotic membrane:	n/a
43	chr16:30394532-30394582	SK-N-SH_RA	brain:	n/a
44	chr16:30394532-30394582	GM19239	blood:	n/a
45	chr16:30394532-30394582	SKMC	muscle:	n/a
46	chr16:30394532-30394582	HCT-116	colon:	n/a
47	chr16:30394532-30394582	Hela-S3	cervix:	n/a
48	chr16:30394532-30394582	K562	blood:	n/a
49	chr16:30394532-30394582	NHBE	bronchial:	n/a
50	chr16:30394532-30394582	AoSMC	blood vessel:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr16:30389715..30395001-chr16:30417296..30421020,7	K562	blood:
2	chr16:30386182..30395144-chr16:30402818..30414477,44	MCF-7	breast:
3	chr16:30387676..30396507-chr16:30404234..30411930,28	K562	blood:
4	chr16:30393486..30397071-chr16:30402673..30407150,6	MCF-7	breast:
5	chr16:30384243..30394929-chr16:30405602..30409736,14	K562	blood:

No data

Variant related genes	Relation type
SEPT1	TF binding region
ENSG00000270466	TF binding region
SEPT1	CpG island
ENSG00000270466	CpG island
ENSG00000179965	Chromatin interaction
ENSG00000180096	Chromatin interaction
ENSG00000180035	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11642676	0.87[EUR][1000 genomes]
rs11645581	0.82[EUR][1000 genomes]
rs11646130	0.87[EUR][1000 genomes]
rs11862806	0.81[EUR][1000 genomes]
rs11863150	0.84[EUR][1000 genomes]
rs12446288	0.86[EUR][1000 genomes]
rs12447833	0.91[EUR][1000 genomes]
rs35480350	0.86[EUR][1000 genomes]
rs4787642	0.84[EUR][1000 genomes]
rs4787643	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4788409	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4788410	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4788411	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4788413	0.84[EUR][1000 genomes]
rs62055459	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6565180	0.81[EUR][1000 genomes]
rs6565182	0.88[EUR][1000 genomes]
rs6565183	0.83[EUR][1000 genomes]
rs7203359	0.87[EUR][1000 genomes]
rs73532600	0.86[EUR][1000 genomes]
rs8046445	0.85[EUR][1000 genomes]
rs8049108	0.83[EUR][1000 genomes]
rs8060853	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv1056897	chr16:30363683-30457504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv905724	chr16:30368591-30438930	Enhancers Flanking Active TSS Active TSS Weak transcription 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	61 gene(s)	inside rSNPs	diseases
5	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
6	nsv827612	chr16:30371538-30429862	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
7	nsv905725	chr16:30376959-30420851	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
8	nsv962197	chr16:30390489-30425618	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv1782	chr16:30391812-30410266	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9921711	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL
rs9921711	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30390800-30395200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr16:30390800-30405600	Weak transcription	Right Atrium	heart
3	chr16:30391000-30395000	Weak transcription	Fetal Lung	lung
4	chr16:30391000-30405000	Weak transcription	NHLF	lung
5	chr16:30391000-30405200	Weak transcription	Fetal Brain Female	brain
6	chr16:30391000-30405400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr16:30391400-30396800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr16:30392000-30395800	Enhancers	Fetal Muscle Trunk	muscle
9	chr16:30392200-30394600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr16:30392200-30394600	Flanking Active TSS	GM12878-XiMat	blood
11	chr16:30392200-30395000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr16:30392200-30395600	Enhancers	Fetal Muscle Leg	muscle
13	chr16:30392400-30394600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr16:30392400-30394800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr16:30392400-30397800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr16:30392600-30395200	Flanking Active TSS	Dnd41	blood
17	chr16:30393000-30394600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr16:30393000-30394600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr16:30393000-30394800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr16:30393200-30394600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr16:30393200-30394800	Weak transcription	Fetal Stomach	stomach
22	chr16:30394000-30394600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr16:30394000-30395000	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr16:30394200-30395200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr16:30394200-30395400	Enhancers	Stomach Smooth Muscle	stomach
26	chr16:30394200-30395800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr16:30394400-30394800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr16:30394400-30395000	Enhancers	Primary B cells from cord blood	blood
29	chr16:30394400-30395000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr16:30394400-30395200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr16:30394400-30395200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr16:30394400-30395200	Weak transcription	Colonic Mucosa	Colon
33	chr16:30394400-30395400	Enhancers	Primary B cells from peripheral blood	blood
34	chr16:30394400-30395400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr16:30394400-30395400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr16:30394400-30395400	Enhancers	Thymus	Thymus
37	chr16:30394400-30395600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr16:30394400-30395600	Enhancers	Fetal Thymus	thymus

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