Variant report

Variant	rs930100
Chromosome Location	chr19:39544234-39544235
allele	G/T
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	EGR1	chr19:39544166-39544362	K562	blood:	n/a	n/a
2	EGR1	chr19:39544186-39544345	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39543748..39546255-chr19:39599767..39602313,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251709	TF binding region

Extended variants
information (count: 81 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10409280	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10411234	0.89[ASN][1000 genomes]
rs10411271	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12151099	0.92[ASN][1000 genomes]
rs12463075	0.82[ASN][1000 genomes]
rs12609401	0.84[ASN][1000 genomes]
rs12974080	0.91[ASN][1000 genomes]
rs12974708	0.98[ASN][1000 genomes]
rs12975482	0.99[ASN][1000 genomes]
rs12976100	0.98[ASN][1000 genomes]
rs12979968	0.86[ASN][1000 genomes]
rs12981133	0.84[ASN][1000 genomes]
rs12982067	0.89[ASN][1000 genomes]
rs12983005	0.93[ASN][1000 genomes]
rs12983352	0.89[ASN][1000 genomes]
rs12983682	0.92[ASN][1000 genomes]
rs12984833	0.97[ASN][1000 genomes]
rs12984836	0.97[ASN][1000 genomes]
rs13345897	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1626050	0.84[ASN][1000 genomes]
rs1627631	0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1628376	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1628426	0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1629253	0.84[ASN][1000 genomes]
rs1651747	0.84[ASN][1000 genomes]
rs16973058	0.82[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs17795157	0.80[JPT][hapmap]
rs1864186	0.88[ASN][1000 genomes]
rs1864188	0.88[ASN][1000 genomes]
rs1869982	0.87[ASN][1000 genomes]
rs2318897	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34240661	0.87[ASN][1000 genomes]
rs35622111	0.82[ASN][1000 genomes]
rs4802010	0.86[ASN][1000 genomes]
rs482342	0.80[JPT][hapmap]
rs483359	0.80[JPT][hapmap]
rs487356	0.84[ASN][1000 genomes]
rs498586	0.81[JPT][hapmap]
rs500660	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs500691	0.85[JPT][hapmap]
rs516901	0.84[ASN][1000 genomes]
rs523890	0.88[ASN][1000 genomes]
rs523943	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs542464	0.82[ASN][1000 genomes]
rs553330	0.84[ASN][1000 genomes]
rs554932	0.84[ASN][1000 genomes]
rs561148	0.82[ASN][1000 genomes]
rs561329	0.82[ASN][1000 genomes]
rs564474	0.80[JPT][hapmap]
rs572764	0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs57401831	0.82[ASN][1000 genomes]
rs57724551	0.86[ASN][1000 genomes]
rs582575	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs582593	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs583529	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs583995	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs584806	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs584822	0.84[ASN][1000 genomes]
rs586107	0.82[ASN][1000 genomes]
rs586176	0.84[ASN][1000 genomes]
rs59698424	0.83[ASN][1000 genomes]
rs598468	0.86[ASN][1000 genomes]
rs599230	0.84[ASN][1000 genomes]
rs602899	0.84[ASN][1000 genomes]
rs61553368	0.91[ASN][1000 genomes]
rs618068	0.84[ASN][1000 genomes]
rs62119464	0.86[ASN][1000 genomes]
rs62119508	0.85[ASN][1000 genomes]
rs62119510	0.90[ASN][1000 genomes]
rs662202	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs678772	0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs678848	0.84[ASN][1000 genomes]
rs678885	0.80[JPT][hapmap]
rs679657	0.84[ASN][1000 genomes]
rs679732	0.84[ASN][1000 genomes]
rs681145	0.80[JPT][hapmap]
rs7246076	0.81[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	nsv963126	chr19:39521120-39552490	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2760517	chr19:39530012-39544234	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs930100	CTB-189B5.3	cis	Skin Sun Exposed Lower leg	GTEx
rs930100	LOC390940	cis	cerebellum	SCAN
rs930100	GRIK5	cis	cerebellum	SCAN
rs930100	PSG3	cis	cerebellum	SCAN
rs930100	CTB-189B5.3	cis	Esophagus Mucosa	GTEx
rs930100	GLTSCR1	cis	cerebellum	SCAN
rs930100	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx
rs930100	ZNF155	cis	parietal	SCAN
rs930100	PSG2	cis	cerebellum	SCAN
rs930100	ZFP112	cis	parietal	SCAN
rs930100	FBXO27	cis	Esophagus Mucosa	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39541200-39546400	Weak transcription	Right Atrium	heart
2	chr19:39542200-39546600	Enhancers	Fetal Intestine Large	intestine
3	chr19:39543000-39544400	Enhancers	A549	lung
4	chr19:39543000-39544800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr19:39543000-39544800	Enhancers	Brain Cingulate Gyrus	brain
6	chr19:39543000-39545200	Enhancers	Brain Anterior Caudate	brain
7	chr19:39543000-39545200	Enhancers	Fetal Intestine Small	intestine
8	chr19:39543000-39545600	Enhancers	Stomach Mucosa	stomach
9	chr19:39543200-39544800	Enhancers	Brain Angular Gyrus	brain
10	chr19:39543200-39544800	Enhancers	Brain Hippocampus Middle	brain
11	chr19:39543200-39544800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:39543200-39545200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:39543200-39545200	Enhancers	Brain Substantia Nigra	brain
14	chr19:39543400-39544800	Enhancers	Duodenum Mucosa	Duodenum
15	chr19:39543800-39544400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:39543800-39544400	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr19:39544000-39544800	Flanking Active TSS	HepG2	liver
18	chr19:39544200-39544400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr19:39544200-39544600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links