Variant report

Variant	rs1925715
Chromosome Location	chr1:228703444-228703445
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	chr1:228702810-228703476	HCT-116	colon:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
2	RAD21	chr1:228702832-228703459	A549	lung:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
3	CTCF	chr1:228702899-228703451	MCF-7	breast:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
4	RAD21	chr1:228702762-228703474	HCT-116	colon:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
5	RAD21	chr1:228702799-228703492	A549	lung:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
6	CTCF	chr1:228703399-228703530	GM10248	blood:	n/a	n/a
7	CTCF	chr1:228702571-228703529	A549	lung:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
8	CTCF	chr1:228703360-228703510	GM12868	blood:	n/a	n/a
9	CTCF	chr1:228703428-228703477	Medullo	brain:	n/a	n/a
10	GATA1	chr1:228699888-228703545	K562	blood:	n/a	chr1:228701158-228701168
11	CTCF	chr1:228702672-228703588	SK-N-SH	brain:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
12	CTCF	chr1:228703340-228703490	AG04449	skin:	n/a	n/a
13	CTCF	chr1:228702890-228703466	HCT-116	colon:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
14	CTCF	chr1:228702681-228703493	HCT-116	colon:	n/a	chr1:228703152-228703173 chr1:228703159-228703172 chr1:228703157-228703175 chr1:228703065-228703086 chr1:228703072-228703085
15	RAD21	chr1:228702623-228703787	SK-N-SH	brain:	n/a	chr1:228703158-228703171 chr1:228703157-228703169 chr1:228703074-228703083 chr1:228703155-228703174
16	CTCF	chr1:228703300-228703450	GM12874	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228638761..228647671-chr1:228695176..228704605,18	K562	blood:
2	chr1:228696529..228699343-chr1:228702490..228705353,2	K562	blood:
3	chr1:228191722..228192636-chr1:228703111..228703660,2	K562	blood:
4	chr1:228456017..228456963-chr1:228702685..228703640,2	K562	blood:
5	chr1:228659611..228660330-chr1:228702674..228703564,2	K562	blood:
6	chr1:228452377..228453300-chr1:228702937..228703662,2	K562	blood:
7	chr1:228392725..228394871-chr1:228701724..228704719,2	K562	blood:
8	chr1:228688493..228689315-chr1:228702705..228703594,3	MCF-7	breast:
9	chr1:228528158..228528703-chr1:228703089..228703660,2	K562	blood:
10	chr1:228414817..228415566-chr1:228702553..228703686,3	K562	blood:
11	chr1:228645121..228649502-chr1:228703257..228706050,4	MCF-7	breast:
12	chr1:228353333..228353944-chr1:228702817..228703586,2	K562	blood:
13	chr1:228688334..228689291-chr1:228702696..228703587,3	K562	blood:
14	chr1:228400895..228401787-chr1:228702783..228703634,3	K562	blood:

Variant related genes	Relation type
BTNL10	TF binding region
ENSG00000181873	Chromatin interaction
ENSG00000162913	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000181218	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10916331	0.90[JPT][hapmap]
rs10916348	0.94[CHB][hapmap]
rs12028234	0.89[ASN][1000 genomes]
rs12044013	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12045742	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12046644	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12161195	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12161347	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12563568	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13374918	0.87[YRI][hapmap]
rs1925723	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4344301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61825663	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61825664	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61827306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61827315	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61827317	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61827321	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6426509	0.85[JPT][hapmap]
rs6672815	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs6681216	1.00[CHB][hapmap]
rs942850	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
5	nsv549297	chr1:228681195-228720480	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv468305	chr1:228681195-228731677	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv549298	chr1:228681195-228731677	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv947521	chr1:228698244-228704499	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1925715	FAM177B	cis	parietal	SCAN
rs1925715	ENAH	cis	cerebellum	SCAN
rs1925715	TP53BP2	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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