Variant report

Variant	rs12671598
Chromosome Location	chr7:50654168-50654169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50650775..50655570-chr7:50656344..50660954,5	K562	blood:
2	chr7:50651220..50655570-chr7:50655911..50660457,6	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10265930	0.82[EUR][1000 genomes]
rs10899748	0.99[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11976778	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11977415	0.89[AFR][1000 genomes]
rs12666409	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12673638	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1470747	0.81[EUR][1000 genomes]
rs2329346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28415418	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56105337	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56661863	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66792686	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68011952	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7790919	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7807335	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs978784	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1032882	chr7:50611138-50775257	Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538834	chr7:50611138-50775257	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1031138	chr7:50651793-50814881	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12671598	FIGNL1	cis	lung	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50650800-50659600	Weak transcription	Ovary	ovary
2	chr7:50652000-50671800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr7:50652200-50657800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:50652400-50687400	Weak transcription	Right Atrium	heart
5	chr7:50652600-50655400	Weak transcription	Thymus	Thymus
6	chr7:50652600-50658600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr7:50652800-50658400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:50652800-50660400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:50653000-50655800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr7:50653000-50658800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr7:50653000-50659800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:50653000-50660000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr7:50653200-50672400	Weak transcription	NHEK	skin
14	chr7:50653400-50656800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:50653400-50659800	Weak transcription	Fetal Lung	lung
16	chr7:50653400-50670600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr7:50653600-50654400	Enhancers	Pancreas	Pancrea
18	chr7:50653600-50654800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:50653600-50656800	Weak transcription	Placenta	Placenta
20	chr7:50654000-50680000	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links