Variant report

Variant	rs4886921
Chromosome Location	chr15:78114116-78114117
allele	C/T
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	SMC3	chr15:78113113-78114476	SK-N-SH	brain:	n/a	chr15:78113984-78113998
2	MAZ	chr15:78113832-78114140	K562	blood:	n/a	n/a
3	SMC3	chr15:78113640-78114179	K562	blood:	n/a	chr15:78113984-78113998
4	CTCF	chr15:78113875-78114121	LNCaP	prostate:	n/a	chr15:78113982-78114000
5	CTCF	chr15:78113754-78114152	K562	blood:	n/a	chr15:78113982-78114000
6	RAD21	chr15:78113807-78114173	K562	blood:	n/a	chr15:78113980-78113999
7	CTCF	chr15:78113855-78114146	MCF-7	breast:	n/a	chr15:78113982-78114000
8	CTCF	chr15:78113751-78114144	T-47D	breast:	n/a	chr15:78113982-78114000
9	BHLHE40	chr15:78113815-78114121	K562	blood:	n/a	chr15:78113828-78113844
10	RAD21	chr15:78113782-78114182	Hela-S3	cervix:	n/a	chr15:78113980-78113999
11	CTCF	chr15:78113768-78114188	K562	blood:	n/a	chr15:78113982-78114000
12	CTCF	chr15:78113751-78114177	T-47D	breast:	n/a	chr15:78113982-78114000
13	ZNF143	chr15:78113824-78114155	H1-hESC	embryonic stem cell:	n/a	n/a
14	ZNF143	chr15:78113842-78114137	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr15:78113820-78114194	ECC-1	luminal epithelium:	n/a	chr15:78113982-78114000
16	ZNF263	chr15:78111583-78114384	HEK293-T-REx	kidney:	n/a	chr15:78113198-78113207
17	RCOR1	chr15:78113932-78114129	K562	blood:	n/a	n/a
18	CTCF	chr15:78113746-78114209	H1-hESC	embryonic stem cell:	n/a	chr15:78113982-78114000
19	RAD21	chr15:78113753-78114261	MCF-7	breast:	n/a	chr15:78113980-78113999
20	CTCF	chr15:78113705-78114256	A549	lung:	n/a	chr15:78113982-78114000
21	CTCF	chr15:78113841-78114143	NHEK	skin:	n/a	chr15:78113982-78114000
22	CTCF	chr15:78113849-78114140	A549	lung:	n/a	chr15:78113982-78114000
23	CTCF	chr15:78113850-78114154	Fibrobl	skin:	n/a	chr15:78113982-78114000
24	RAD21	chr15:78113815-78114175	A549	lung:	n/a	chr15:78113980-78113999
25	CTCF	chr15:78112223-78114736	SK-N-SH	brain:	n/a	chr15:78112615-78112628 chr15:78112615-78112624 chr15:78112771-78112781 chr15:78113982-78114000
26	CTCF	chr15:78113777-78114208	K562	blood:	n/a	chr15:78113982-78114000
27	JUND	chr15:78113836-78114155	K562	blood:	n/a	n/a
28	RAD21	chr15:78113634-78114250	MCF-7	breast:	n/a	chr15:78113980-78113999
29	CTCF	chr15:78113871-78114151	GM10266	blood:	n/a	chr15:78113982-78114000
30	RAD21	chr15:78113613-78114264	A549	lung:	n/a	chr15:78113980-78113999
31	RAD21	chr15:78113623-78114218	SK-N-SH_RA	brain:	n/a	chr15:78113980-78113999
32	RAD21	chr15:78113646-78114217	H1-hESC	embryonic stem cell:	n/a	chr15:78113980-78113999
33	CTCF	chr15:78113842-78114135	Medullo	brain:	n/a	chr15:78113982-78114000
34	CTCF	chr15:78113868-78114132	GM10248	blood:	n/a	chr15:78113982-78114000
35	SMC3	chr15:78113822-78114170	GM12878	blood:	n/a	chr15:78113984-78113998
36	RAD21	chr15:78113778-78114178	GM12878	blood:	n/a	chr15:78113980-78113999
37	MAZ	chr15:78113884-78114117	Hela-S3	cervix:	n/a	n/a
38	CTCF	chr15:78113851-78114139	Hela-S3	cervix:	n/a	chr15:78113982-78114000
39	SMC3	chr15:78113789-78114172	Hela-S3	cervix:	n/a	chr15:78113984-78113998
40	RAD21	chr15:78113780-78114206	HepG2	liver:	n/a	chr15:78113980-78113999
41	CTCF	chr15:78113980-78114130	GM12869	blood:	n/a	chr15:78113982-78114000
42	RAD21	chr15:78113756-78114214	HepG2	liver:	n/a	chr15:78113980-78113999
43	RAD21	chr15:78113618-78114297	ECC-1	luminal epithelium:	n/a	chr15:78113980-78113999
44	RAD21	chr15:78113697-78114167	H1-hESC	embryonic stem cell:	n/a	chr15:78113980-78113999
45	POLR2A	chr15:78111620-78118444	SK-N-MC	brain:	n/a	n/a
46	CTCF	chr15:78113849-78114138	ECC-1	luminal epithelium:	n/a	chr15:78113982-78114000
47	CTCF	chr15:78113784-78114173	K562	blood:	n/a	chr15:78113982-78114000
48	RAD21	chr15:78113767-78114209	H1-hESC	embryonic stem cell:	n/a	chr15:78113980-78113999
49	CTCF	chr15:78113860-78114148	Spleen_OC	spleen:	n/a	chr15:78113982-78114000
50	CTCF	chr15:78113596-78114250	HCT-116	colon:	n/a	chr15:78113982-78114000

No.	Distal block	Cell Line	Cell type
1	chr15:77411244..77411752-chr15:78113897..78114465,2	K562	blood:
2	chr15:77923251..77928296-chr15:78111448..78115771,8	MCF-7	breast:
3	chr15:78109668..78112280-chr15:78112604..78115106,3	MCF-7	breast:
4	chr15:77925397..77928069-chr15:78112259..78116246,3	K562	blood:
5	chr15:77951785..77952749-chr15:78113535..78114168,4	MCF-7	breast:
6	chr15:77950482..77951067-chr15:78113646..78114389,2	K562	blood:
7	chr15:77925397..77927315-chr15:78112259..78115116,2	K562	blood:
8	chr15:77951840..77952665-chr15:78112887..78114250,4	MCF-7	breast:
9	chr15:77925435..77927439-chr15:78112259..78115090,22	K562	blood:
10	chr15:77925072..77927787-chr15:78111223..78115888,59	MCF-7	breast:
11	chr15:77951738..77952728-chr15:78113529..78114461,5	K562	blood:
12	chr15:77835732..77836546-chr15:78113747..78114395,2	MCF-7	breast:
13	chr15:77925249..77927257-chr15:78113205..78115049,24	MCF-7	breast:

Variant related genes	Relation type
LINGO1	TF binding region
ENSG00000259281	Chromatin interaction
ENSG00000169783	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11631685	0.86[ASN][1000 genomes]
rs12441652	0.82[ASN][1000 genomes]
rs35130910	0.81[ASN][1000 genomes]
rs3902958	0.85[ASN][1000 genomes]
rs4243051	0.87[ASN][1000 genomes]
rs4426322	0.84[ASN][1000 genomes]
rs4886914	0.81[ASN][1000 genomes]
rs5021303	0.82[CEU][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.81[ASN][1000 genomes]
rs8025494	0.86[ASN][1000 genomes]
rs8026726	0.83[CEU][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.81[ASN][1000 genomes]
rs8031991	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv833061	chr15:77998374-78121905	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv833062	chr15:78035206-78220358	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv904421	chr15:78041789-78129964	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv904423	chr15:78059488-78119345	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv904424	chr15:78059488-78158893	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv471255	chr15:78063585-78131097	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv570171	chr15:78064664-78131097	Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv904425	chr15:78064664-78153850	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
14	nsv904426	chr15:78090630-78264164	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	esv1806493	chr15:78106177-78119345	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv1796951	chr15:78111223-78119345	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv1849555	chr15:78111223-78119345	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	esv1813777	chr15:78111702-78119345	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4886921	TMED3	cis	cerebellum	SCAN
rs4886921	CHRNA5	cis	parietal	SCAN
rs4886921	CPLX3	cis	parietal	SCAN
rs4886921	MYO9A	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78112000-78114200	Bivalent Enhancer	Placenta	Placenta
2	chr15:78112600-78114600	Bivalent Enhancer	Fetal Muscle Leg	muscle
3	chr15:78112600-78115800	Bivalent Enhancer	Fetal Intestine Small	intestine
4	chr15:78112800-78114200	Weak transcription	Right Atrium	heart
5	chr15:78113000-78114200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:78113400-78114600	Enhancers	Fetal Brain Male	brain
7	chr15:78113600-78114400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:78113600-78114400	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr15:78113800-78114400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr15:78113800-78116200	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:78114000-78114400	Flanking Active TSS	Fetal Brain Female	brain

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