Variant report

Variant	rs2999539
Chromosome Location	chr1:151986627-151986628
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:151985598-151986661	MCF-7	breast:	n/a	chr1:151986298-151986316
2	CTCF	chr1:151986605-151986660	K562	blood:	n/a	n/a
3	CTCF	chr1:151986600-151986639	Gliobla	brain:	n/a	n/a
4	CTCF	chr1:151985923-151986628	HCT-116	colon:	n/a	chr1:151986298-151986316
5	CTCF	chr1:151986591-151986696	GM20000	blood:	n/a	n/a
6	CTCF	chr1:151985949-151986908	A549	lung:	n/a	chr1:151986298-151986316
7	RAD21	chr1:151985889-151986630	MCF-7	breast:	n/a	chr1:151986296-151986315
8	SMC3	chr1:151985595-151986670	SK-N-SH	brain:	n/a	chr1:151986300-151986314
9	CTCF	chr1:151986480-151986630	GM12867	blood:	n/a	n/a
10	CTCF	chr1:151986580-151986730	GM12874	blood:	n/a	n/a
11	CTCF	chr1:151986600-151986750	HBMEC	blood vessel:	n/a	n/a
12	CTCF	chr1:151986620-151986770	GM12870	blood:	n/a	n/a
13	CTCF	chr1:151986540-151986690	HepG2	liver:	n/a	n/a
14	CTCF	chr1:151986620-151986770	NHEK	skin:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151964978..151966763-chr1:151984621..151987442,2	K562	blood:
2	chr1:151857351..151860092-chr1:151985508..151987866,2	MCF-7	breast:
3	chr1:151976242..151977190-chr1:151986239..151986739,2	MCF-7	breast:
4	chr1:151880783..151882439-chr1:151984923..151987759,2	MCF-7	breast:
5	chr1:151978814..151981429-chr1:151985476..151987794,2	K562	blood:
6	chr1:151976342..151977102-chr1:151985791..151986707,2	MCF-7	breast:
7	chr1:151940589..151941111-chr1:151986094..151986796,2	K562	blood:
8	chr1:151881612..151883127-chr1:151984846..151987615,2	MCF-7	breast:
9	chr1:151973932..151974613-chr1:151985782..151987112,4	MCF-7	breast:
10	chr1:151985750..151986659-chr1:152155001..152155545,2	MCF-7	breast:
11	chr1:151906193..151906890-chr1:151985331..151986972,5	MCF-7	breast:
12	chr1:151861451..151862101-chr1:151985405..151986706,6	MCF-7	breast:
13	chr1:151906192..151907068-chr1:151986048..151986722,4	MCF-7	breast:
14	chr1:151986485..151988607-chr1:151992304..151995986,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000240667	TF binding region
ENSG00000197747	Chromatin interaction
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1038747	0.88[JPT][hapmap]
rs10788820	0.81[JPT][hapmap]
rs11204922	0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs11542015	0.80[AMR][1000 genomes]
rs12083193	0.81[CHB][hapmap];0.89[TSI][hapmap]
rs12116923	0.85[JPT][hapmap]
rs12410789	0.87[ASN][1000 genomes]
rs1532133	0.95[CHB][hapmap]
rs16833728	0.84[TSI][hapmap]
rs16833743	0.81[CHB][hapmap]
rs1979637	0.90[CHB][hapmap]
rs1994606	0.84[ASN][1000 genomes]
rs2279501	0.85[JPT][hapmap]
rs2279502	0.85[JPT][hapmap]
rs2338019	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2932570	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932574	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932590	0.83[ASW][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2999526	0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2999528	0.83[ASW][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2999531	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs2999534	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2999560	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999561	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007708	0.83[ASW][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3791153	0.81[CHB][hapmap]
rs6587640	0.81[CHB][hapmap];0.84[TSI][hapmap]
rs6678672	0.81[CHB][hapmap];0.87[TSI][hapmap]
rs7541099	0.84[TSI][hapmap]
rs902313	0.84[TSI][hapmap]
rs971887	0.84[TSI][hapmap]

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	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2999539	THEM4	cis	multi-tissue	Pritchard
rs2999539	THEM4	cis	lymphoblastoid	seeQTL
rs2999539	THEM4	cis	Esophagus Muscularis	GTEx
rs2999539	NBPF18P	cis	Nerve Tibial	GTEx
rs2999539	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs2999539	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs2999539	S100A10	cis	lymphoblastoid	seeQTL
rs2999539	S100A10	cis	multi-tissue	Pritchard
rs2999539	S100A10	cis	Lymphoblastoid	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151976800-151993600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:151985800-151986800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr1:151985800-151986800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr1:151986000-151986800	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr1:151986000-151986800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:151986000-151986800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:151986200-151989800	Enhancers	HMEC	breast
8	chr1:151986400-151986800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:151986400-151986800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:151986400-151986800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:151986400-151986800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:151986400-151988200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:151986600-151987400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:151986600-151987600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:151986600-151987800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:151986600-151988000	Weak transcription	NHEK	skin
17	chr1:151986600-151996200	Weak transcription	H9 Cell Line	embryonic stem cell

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