Variant report

Variant	rs17355921
Chromosome Location	chr7:12623620-12623621
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	RFX5	chr7:12623599-12623960	Hela-S3	cervix:	n/a	n/a
2	FOXA1	chr7:12623563-12623881	T-47D	breast:	n/a	chr7:12623792-12623807
3	GATA3	chr7:12623390-12624063	MCF-7	breast:	n/a	chr7:12623743-12623764
4	GATA3	chr7:12623597-12623888	MCF-7	breast:	n/a	chr7:12623743-12623764
5	NR2F2	chr7:12623383-12624056	MCF-7	breast:	n/a	n/a
6	GATA3	chr7:12623503-12623875	A549	lung:	n/a	chr7:12623743-12623764
7	GATA3	chr7:12623525-12623873	T-47D	breast:	n/a	chr7:12623743-12623764
8	CEBPB	chr7:12623582-12623862	Hela-S3	cervix:	n/a	n/a
9	NR2F2	chr7:12623457-12623974	MCF-7	breast:	n/a	n/a
10	GATA3	chr7:12623300-12624108	MCF-7	breast:	n/a	chr7:12623743-12623764
11	GATA3	chr7:12623441-12624120	A549	lung:	n/a	chr7:12623743-12623764
12	FOXA1	chr7:12623562-12623887	T-47D	breast:	n/a	chr7:12623792-12623807
13	FOXA2	chr7:12623620-12623848	HepG2	liver:	n/a	n/a
14	HDAC2	chr7:12623505-12623986	MCF-7	breast:	n/a	n/a
15	SIN3AK20	chr7:12623490-12624069	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:12620852..12624352-chr7:12625661..12628427,3	K562	blood:

Variant related genes	Relation type
SCIN	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1034856	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1118998	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11558844	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11973033	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17283717	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240572	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2240574	0.81[ASN][1000 genomes]
rs3735222	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3735223	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41356146	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41379149	0.81[ASN][1000 genomes]
rs4458754	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55682719	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55829483	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55999874	0.81[ASN][1000 genomes]
rs56085455	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56131067	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56274604	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56760264	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57778115	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6460964	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6961909	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6965970	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6967031	0.94[ASN][1000 genomes]
rs6972418	0.81[ASN][1000 genomes]
rs73060662	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73060664	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73060678	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73060679	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73060680	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73060684	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73060686	0.81[ASN][1000 genomes]
rs73062610	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73062611	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73062639	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7782451	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7799976	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7803810	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7804260	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7811582	0.81[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	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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	58 gene(s)	inside rSNPs	diseases
4	nsv1021371	chr7:12530491-12710429	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1017577	chr7:12530491-12722947	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1030764	chr7:12532287-12710429	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1018053	chr7:12580554-12632996	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1020242	chr7:12605593-12641202	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17355921	SCIN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12611800-12637600	Weak transcription	Colonic Mucosa	Colon
2	chr7:12613200-12624200	Weak transcription	Adipose Nuclei	Adipose
3	chr7:12619800-12630400	Weak transcription	Esophagus	oesophagus
4	chr7:12620600-12624400	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr7:12620600-12626600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr7:12620800-12623800	Weak transcription	Small Intestine	intestine
7	chr7:12620800-12624600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:12620800-12625800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:12621800-12625600	Enhancers	Hela-S3	cervix
10	chr7:12622000-12624400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:12622000-12624600	Enhancers	Osteobl	bone
12	chr7:12622000-12625600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:12622600-12625000	Enhancers	Duodenum Mucosa	Duodenum
14	chr7:12622800-12624400	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr7:12622800-12624400	Enhancers	K562	blood
16	chr7:12623000-12624400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:12623000-12624400	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr7:12623000-12625200	Enhancers	Stomach Mucosa	stomach
19	chr7:12623200-12624600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:12623400-12624400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr7:12623400-12624600	Weak transcription	Gastric	stomach
22	chr7:12623400-12624600	Weak transcription	NHDF-Ad	bronchial
23	chr7:12623400-12624800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr7:12623400-12628000	Weak transcription	Placenta	Placenta
25	chr7:12623600-12624600	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links