Variant report

Variant	rs12441953
Chromosome Location	chr15:78113831-78113832
allele	A/C
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	SMC3	chr15:78113640-78114179	K562	blood:	n/a	chr15:78113984-78113998
3	CTCF	chr15:78113754-78114152	K562	blood:	n/a	chr15:78113982-78114000
4	RAD21	chr15:78113807-78114173	K562	blood:	n/a	chr15:78113980-78113999
5	CTCF	chr15:78113751-78114144	T-47D	breast:	n/a	chr15:78113982-78114000
6	BHLHE40	chr15:78113815-78114121	K562	blood:	n/a	chr15:78113828-78113844
7	RAD21	chr15:78113782-78114182	Hela-S3	cervix:	n/a	chr15:78113980-78113999
8	CTCF	chr15:78113768-78114188	K562	blood:	n/a	chr15:78113982-78114000
9	CTCF	chr15:78113751-78114177	T-47D	breast:	n/a	chr15:78113982-78114000
10	ZNF143	chr15:78113824-78114155	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr15:78113820-78114194	ECC-1	luminal epithelium:	n/a	chr15:78113982-78114000
12	ZNF263	chr15:78111583-78114384	HEK293-T-REx	kidney:	n/a	chr15:78113198-78113207
13	CTCF	chr15:78113746-78114209	H1-hESC	embryonic stem cell:	n/a	chr15:78113982-78114000
14	RAD21	chr15:78113753-78114261	MCF-7	breast:	n/a	chr15:78113980-78113999
15	CTCF	chr15:78113705-78114256	A549	lung:	n/a	chr15:78113982-78114000
16	RAD21	chr15:78113815-78114175	A549	lung:	n/a	chr15:78113980-78113999
17	CTCF	chr15:78112223-78114736	SK-N-SH	brain:	n/a	chr15:78112615-78112628 chr15:78112615-78112624 chr15:78112771-78112781 chr15:78113982-78114000
18	CTCF	chr15:78113777-78114208	K562	blood:	n/a	chr15:78113982-78114000
19	RAD21	chr15:78113634-78114250	MCF-7	breast:	n/a	chr15:78113980-78113999
20	RAD21	chr15:78113613-78114264	A549	lung:	n/a	chr15:78113980-78113999
21	RAD21	chr15:78113804-78114048	GM12878	blood:	n/a	chr15:78113980-78113999
22	RAD21	chr15:78113623-78114218	SK-N-SH_RA	brain:	n/a	chr15:78113980-78113999
23	RAD21	chr15:78113646-78114217	H1-hESC	embryonic stem cell:	n/a	chr15:78113980-78113999
24	SMC3	chr15:78113822-78114170	GM12878	blood:	n/a	chr15:78113984-78113998
25	RAD21	chr15:78113778-78114178	GM12878	blood:	n/a	chr15:78113980-78113999
26	SMC3	chr15:78113789-78114172	Hela-S3	cervix:	n/a	chr15:78113984-78113998
27	RAD21	chr15:78113780-78114206	HepG2	liver:	n/a	chr15:78113980-78113999
28	RAD21	chr15:78113756-78114214	HepG2	liver:	n/a	chr15:78113980-78113999
29	RAD21	chr15:78113618-78114297	ECC-1	luminal epithelium:	n/a	chr15:78113980-78113999
30	RAD21	chr15:78113697-78114167	H1-hESC	embryonic stem cell:	n/a	chr15:78113980-78113999
31	POLR2A	chr15:78111620-78118444	SK-N-MC	brain:	n/a	n/a
32	CTCF	chr15:78113720-78113870	A549	lung:	n/a	n/a
33	CTCF	chr15:78113784-78114173	K562	blood:	n/a	chr15:78113982-78114000
34	RAD21	chr15:78113767-78114209	H1-hESC	embryonic stem cell:	n/a	chr15:78113980-78113999
35	CTCF	chr15:78113596-78114250	HCT-116	colon:	n/a	chr15:78113982-78114000
36	CTCF	chr15:78113826-78114143	GM19238	blood:	n/a	chr15:78113982-78114000
37	CTCF	chr15:78113629-78114268	MCF-7	breast:	n/a	chr15:78113982-78114000
38	CTCF	chr15:78113749-78114162	HepG2	liver:	n/a	chr15:78113982-78114000
39	CTCF	chr15:78113772-78114159	A549	lung:	n/a	chr15:78113982-78114000
40	CTCF	chr15:78113783-78114184	GM12878	blood:	n/a	chr15:78113982-78114000
41	TBL1XR1	chr15:78113824-78114133	K562	blood:	n/a	n/a
42	SMC3	chr15:78113798-78114154	HepG2	liver:	n/a	chr15:78113984-78113998
43	CTCF	chr15:78113817-78114072	HepG2	liver:	n/a	chr15:78113982-78114000
44	CTCF	chr15:78112362-78114448	A549	lung:	n/a	chr15:78112615-78112628 chr15:78112615-78112624 chr15:78112771-78112781 chr15:78113982-78114000
45	RAD21	chr15:78113810-78114081	GM12878	blood:	n/a	chr15:78113980-78113999
46	CTCF	chr15:78113744-78114186	H1-hESC	embryonic stem cell:	n/a	chr15:78113982-78114000
47	CTCF	chr15:78113606-78114288	MCF-7	breast:	n/a	chr15:78113982-78114000
48	CTCF	chr15:78113783-78114188	IMR90	lung:	n/a	chr15:78113982-78114000
49	FOXP2	chr15:78113782-78114145	SK-N-MC	brain:	n/a	n/a
50	RAD21	chr15:78113274-78114475	SK-N-SH	brain:	n/a	chr15:78113980-78113999

No.	Distal block	Cell Line	Cell type
1	chr15:77923251..77928296-chr15:78111448..78115771,8	MCF-7	breast:
2	chr15:78109668..78112280-chr15:78112604..78115106,3	MCF-7	breast:
3	chr15:77925397..77928069-chr15:78112259..78116246,3	K562	blood:
4	chr15:77951785..77952749-chr15:78113535..78114168,4	MCF-7	breast:
5	chr15:77950482..77951067-chr15:78113646..78114389,2	K562	blood:
6	chr15:77925397..77927315-chr15:78112259..78115116,2	K562	blood:
7	chr15:77925299..77927652-chr15:78112444..78114100,3	MCF-7	breast:
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: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11072672	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11072677	0.94[ASN][1000 genomes]
rs11072678	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11852404	0.83[ASN][1000 genomes]
rs11852704	0.94[ASN][1000 genomes]
rs11855944	0.83[ASN][1000 genomes]
rs11857499	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11857839	0.87[ASN][1000 genomes]
rs11857968	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11858003	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12441624	0.83[ASN][1000 genomes]
rs12906902	0.83[ASN][1000 genomes]
rs12911998	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12912051	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12914963	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34000202	0.83[ASN][1000 genomes]
rs35265558	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35487286	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4075024	0.87[ASN][1000 genomes]
rs4075981	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4304989	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886913	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4886916	0.83[ASN][1000 genomes]
rs4886923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4886940	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4886945	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56061966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58455314	0.81[EUR][1000 genomes]
rs7164311	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7170767	0.83[ASN][1000 genomes]
rs7175762	0.83[ASN][1000 genomes]
rs7175927	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7181312	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7182069	0.83[ASN][1000 genomes]
rs72730744	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72730767	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72730772	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72730774	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72730775	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	esv3321779	chr15:78109497-78113895	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
17	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
18	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
19	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

No data

Chromatin state (count:20 , 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	chr15:78112800-78114000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
5	chr15:78112800-78114000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
6	chr15:78112800-78114200	Weak transcription	Right Atrium	heart
7	chr15:78113000-78114000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
8	chr15:78113000-78114200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:78113400-78114000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
10	chr15:78113400-78114600	Enhancers	Fetal Brain Male	brain
11	chr15:78113600-78114000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
12	chr15:78113600-78114000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
13	chr15:78113600-78114400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:78113600-78114400	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr15:78113800-78114000	Enhancers	Brain Cingulate Gyrus	brain
16	chr15:78113800-78114000	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:78113800-78114000	Active TSS	Fetal Brain Female	brain
18	chr15:78113800-78114000	Bivalent Enhancer	Stomach Mucosa	stomach
19	chr15:78113800-78114400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr15:78113800-78116200	Weak transcription	Brain Hippocampus Middle	brain

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