Variant report

Variant	rs1727145
Chromosome Location	chr7:99800835-99800836
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr7:99800817-99800952	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr7:99800792-99801026	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:99800831-99800961	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZBTB33	chr7:99800795-99801033	HepG2	liver:	n/a	n/a
5	RXRA	chr7:99800811-99800958	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:99800821-99800947	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99795781..99801540-chr7:99806649..99812120,7	K562	blood:
2	chr7:99799220..99802081-chr7:100025675..100027787,2	K562	blood:
3	chr7:99797808..99801591-chr7:99802250..99804535,3	K562	blood:

No data

Variant related genes	Relation type
STAG3	TF binding region
ENSG00000239521	Chromatin interaction
ENSG00000066923	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000146834	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1043915	0.84[AFR][1000 genomes]
rs10953295	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11764176	0.82[AFR][1000 genomes]
rs11767968	0.82[AFR][1000 genomes]
rs12705073	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13230744	0.83[AFR][1000 genomes]
rs1624099	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1727128	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727129	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727143	0.85[EUR][1000 genomes]
rs1859787	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2246713	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272344	0.82[AFR][1000 genomes]
rs2906646	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2950518	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3735241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3735242	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3779046	0.81[AFR][1000 genomes]
rs4299940	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4729579	0.81[AFR][1000 genomes]
rs4729580	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55796551	0.81[AFR][1000 genomes]
rs6465764	0.81[AFR][1000 genomes]
rs6465766	0.82[AFR][1000 genomes]
rs66809776	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6948729	0.82[AFR][1000 genomes]
rs6960458	0.82[AFR][1000 genomes]
rs705867	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7788301	0.82[AFR][1000 genomes]
rs7799441	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs858502	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs858510	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs941287	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
2	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers 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	1085 gene(s)	inside rSNPs	diseases
3	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
4	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
5	nsv427794	chr7:99750981-99960900	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	nsv428180	chr7:99750981-99960900	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv8182	chr7:99799816-99879781	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1727145	AP4M1	cis	Thyroid	GTEx
rs1727145	PVRIG	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99790000-99808800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr7:99790000-99817000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:99791400-99806800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr7:99793400-99806000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr7:99793600-99805800	Weak transcription	Primary T cells from cord blood	blood
6	chr7:99795600-99812200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:99795800-99802400	Weak transcription	Brain Angular Gyrus	brain
8	chr7:99795800-99807000	Weak transcription	Thymus	Thymus
9	chr7:99796000-99808400	Weak transcription	Brain Anterior Caudate	brain
10	chr7:99796200-99802200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr7:99796400-99808800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr7:99796400-99813000	Weak transcription	Brain Substantia Nigra	brain
13	chr7:99796800-99816800	Weak transcription	Brain Germinal Matrix	brain
14	chr7:99796800-99817000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr7:99798000-99812000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr7:99798200-99801600	Weak transcription	Fetal Muscle Leg	muscle
17	chr7:99798200-99802400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr7:99798200-99804800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:99798200-99806600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr7:99798200-99811200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:99798400-99806200	Weak transcription	Fetal Intestine Small	intestine
22	chr7:99798600-99801400	Weak transcription	GM12878-XiMat	blood
23	chr7:99798600-99802200	Weak transcription	Spleen	Spleen
24	chr7:99798600-99806200	Weak transcription	Fetal Stomach	stomach
25	chr7:99798600-99810400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:99799000-99816600	Weak transcription	Fetal Brain Female	brain
27	chr7:99799200-99806200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr7:99799400-99806200	Weak transcription	Fetal Thymus	thymus
29	chr7:99799600-99808800	Weak transcription	Brain Hippocampus Middle	brain
30	chr7:99799800-99801000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr7:99800200-99812000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr7:99800400-99801000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr7:99800400-99801000	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr7:99800800-99802400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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