Variant report

Variant	rs4886527
Chromosome Location	chr15:78113557-78113558
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	SMC3	chr15:78113113-78114476	SK-N-SH	brain:	n/a	chr15:78113984-78113998
2	CTCF	chr15:78113400-78113690	GM12873	blood:	n/a	n/a
3	CTCF	chr15:78113480-78113630	GM06990	blood:	n/a	n/a
4	ZNF263	chr15:78111583-78114384	HEK293-T-REx	kidney:	n/a	chr15:78113198-78113207
5	CTCF	chr15:78112223-78114736	SK-N-SH	brain:	n/a	chr15:78112615-78112628 chr15:78112615-78112624 chr15:78112771-78112781 chr15:78113982-78114000
6	CTCF	chr15:78113520-78113670	GM12864	blood:	n/a	n/a
7	POLR2A	chr15:78111620-78118444	SK-N-MC	brain:	n/a	n/a
8	CTCF	chr15:78113520-78113670	GM12873	blood:	n/a	n/a
9	CTCF	chr15:78112362-78114448	A549	lung:	n/a	chr15:78112615-78112628 chr15:78112615-78112624 chr15:78112771-78112781 chr15:78113982-78114000
10	RAD21	chr15:78113274-78114475	SK-N-SH	brain:	n/a	chr15:78113980-78113999
11	RAD21	chr15:78113541-78114300	A549	lung:	n/a	chr15:78113980-78113999
12	CTCF	chr15:78113535-78114400	HCT-116	colon:	n/a	chr15:78113982-78114000
13	RAD21	chr15:78113525-78114281	HCT-116	colon:	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	chr15:77925397..77927315-chr15:78112259..78115116,2	K562	blood:
6	chr15:77925299..77927652-chr15:78112444..78114100,3	MCF-7	breast:
7	chr15:77951840..77952665-chr15:78112887..78114250,4	MCF-7	breast:
8	chr15:77925435..77927439-chr15:78112259..78115090,22	K562	blood:
9	chr15:77925072..77927787-chr15:78111223..78115888,59	MCF-7	breast:
10	chr15:77951738..77952728-chr15:78113529..78114461,5	K562	blood:
11	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: 74 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11072674	0.84[ASN][1000 genomes]
rs1123552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11629621	0.84[ASN][1000 genomes]
rs11631822	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11637937	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12591307	0.84[ASN][1000 genomes]
rs12595659	0.86[ASN][1000 genomes]
rs12900865	0.84[ASN][1000 genomes]
rs12901558	0.84[ASN][1000 genomes]
rs12902298	0.84[ASN][1000 genomes]
rs12910504	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12915515	0.84[ASN][1000 genomes]
rs34549121	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34709918	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35020526	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35575866	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3935182	0.86[ASN][1000 genomes]
rs3936093	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4255755	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4420498	0.84[ASN][1000 genomes]
rs4442775	0.85[ASN][1000 genomes]
rs4486846	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4509984	0.84[ASN][1000 genomes]
rs4511491	0.81[ASN][1000 genomes]
rs4542627	0.84[ASN][1000 genomes]
rs4587942	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4589520	0.84[ASN][1000 genomes]
rs4595767	0.84[ASN][1000 genomes]
rs4886526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886531	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886915	0.84[ASN][1000 genomes]
rs4886918	0.95[ASN][1000 genomes]
rs4886919	0.83[AMR][1000 genomes]
rs4886930	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886932	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886939	0.93[ASN][1000 genomes]
rs55726435	0.84[ASN][1000 genomes]
rs61606062	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62007851	0.84[ASN][1000 genomes]
rs6495252	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495253	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7163336	0.81[ASN][1000 genomes]
rs7164558	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7169661	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7176895	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7179211	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7182697	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7183989	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8026203	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8032021	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8036045	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8037968	0.84[ASN][1000 genomes]
rs8039011	0.84[ASN][1000 genomes]
rs8040813	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	esv3375400	chr15:78110347-78113670	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
18	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
19	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
20	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	chr15:78111000-78113600	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr15:78112000-78114200	Bivalent Enhancer	Placenta	Placenta
3	chr15:78112600-78113800	Bivalent/Poised TSS	Fetal Brain Female	brain
4	chr15:78112600-78114600	Bivalent Enhancer	Fetal Muscle Leg	muscle
5	chr15:78112600-78115800	Bivalent Enhancer	Fetal Intestine Small	intestine
6	chr15:78112800-78113600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:78112800-78113600	Bivalent Enhancer	Fetal Heart	heart
8	chr15:78112800-78114000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
9	chr15:78112800-78114000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
10	chr15:78112800-78114200	Weak transcription	Right Atrium	heart
11	chr15:78113000-78113600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
12	chr15:78113000-78113800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
13	chr15:78113000-78114000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
14	chr15:78113000-78114200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:78113200-78113600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
16	chr15:78113200-78113600	Bivalent Enhancer	A549	lung
17	chr15:78113200-78113800	Enhancers	Brain Hippocampus Middle	brain
18	chr15:78113400-78113600	Bivalent Enhancer	Fetal Stomach	stomach
19	chr15:78113400-78114000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
20	chr15:78113400-78114600	Enhancers	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links