Variant report

Variant	rs1531162
Chromosome Location	chr15:75111984-75111985
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMARCC1	chr15:75111020-75112075	Hela-S3	cervix:	n/a	chr15:75111159-75111168

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:75074156..75079604-chr15:75107384..75112501,9	MCF-7	breast:
2	chr15:75109449..75112132-chr15:75112266..75114045,2	MCF-7	breast:
3	chr15:75072350..75078841-chr15:75107920..75114107,12	MCF-7	breast:
4	chr15:75111167..75114133-chr15:75116068..75118230,2	K562	blood:
5	chr15:75108356..75114001-chr15:75126388..75130558,9	MCF-7	breast:
6	chr15:75109652..75112640-chr15:76193633..76196409,2	K562	blood:
7	chr15:75106165..75113668-chr15:75132311..75136608,10	MCF-7	breast:
8	chr15:75110559..75112836-chr15:75746524..75748233,2	K562	blood:
9	chr15:75110223..75112810-chr15:75165268..75167627,2	MCF-7	breast:
10	chr15:75093545..75095294-chr15:75111184..75112969,2	K562	blood:
11	chr15:75080218..75087203-chr15:75106250..75113071,13	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LMAN1L-1	chr15:75111808-75113108	NONHSAT047272

No data

Variant related genes	Relation type
LMAN1L	TF binding region
ENSG00000261606	TF binding region
ENSG00000140474	Chromatin interaction
ENSG00000169375	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000264386	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000140497	Chromatin interaction
ENSG00000261606	Chromatin interaction
ENSG00000167196	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12438333	1.00[CEU][hapmap]
rs12439525	1.00[CEU][hapmap]
rs12439944	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12441444	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12443172	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12593251	0.82[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs12594158	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1531163	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16972714	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2229730	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305667	0.82[CEU][hapmap];0.82[GIH][hapmap]
rs28397782	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28431073	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28577988	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28583379	0.90[ASN][1000 genomes]
rs2899827	1.00[CEU][hapmap];0.92[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3743484	0.81[JPT][hapmap]
rs3743486	1.00[CEU][hapmap];0.92[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3743487	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap]
rs3803568	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886409	1.00[CEU][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs4886620	1.00[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7163332	0.86[TSI][hapmap]
rs7165811	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs8039046	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9796628	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv520527	chr15:75108636-75122856	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75101800-75113200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr15:75107000-75112200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr15:75107200-75112400	Enhancers	Rectal Mucosa Donor 29	rectum
4	chr15:75107200-75114400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:75108000-75113000	Weak transcription	Right Atrium	heart
6	chr15:75108800-75112600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:75109200-75112000	Enhancers	Duodenum Mucosa	Duodenum
8	chr15:75109400-75113800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:75109600-75113200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:75109600-75113600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:75109800-75112000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:75109800-75113000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:75109800-75116800	Weak transcription	Brain Anterior Caudate	brain
14	chr15:75110000-75113000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:75110000-75113000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:75110800-75115000	Enhancers	Primary B cells from peripheral blood	blood
17	chr15:75111000-75112200	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr15:75111000-75113800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr15:75111200-75112200	Flanking Active TSS	Hela-S3	cervix
20	chr15:75111400-75112000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:75111400-75112200	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr15:75111400-75112400	Weak transcription	Esophagus	oesophagus
23	chr15:75111400-75112800	Weak transcription	GM12878-XiMat	blood
24	chr15:75111400-75113200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr15:75111400-75113800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:75111400-75128000	Weak transcription	Gastric	stomach
27	chr15:75111600-75112000	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr15:75111600-75112000	Bivalent Enhancer	HepG2	liver
29	chr15:75111600-75112200	Weak transcription	HSMMtube	muscle
30	chr15:75111600-75113400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr15:75111600-75113600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr15:75111800-75112200	Weak transcription	Spleen	Spleen
33	chr15:75111800-75113200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr15:75111800-75113800	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links