Variant report

Variant	rs4729577
Chromosome Location	chr7:99701640-99701641
allele	C/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	TCF12	chr7:99700701-99701994	SK-N-SH	brain:	n/a	n/a
2	MAZ	chr7:99700719-99701842	IMR90	lung:	n/a	n/a
3	JUND	chr7:99697410-99701902	SK-N-SH	brain:	n/a	chr7:99697600-99697609 chr7:99699066-99699075 chr7:99700947-99700958
4	GATA3	chr7:99701529-99701947	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99697437..99703178-chr7:100024624..100029482,10	K562	blood:
2	chr7:99614250..99615860-chr7:99701481..99703800,2	K562	blood:

Variant related genes	Relation type
AP4M1	TF binding region
MCM7	TF binding region
ENSG00000106261	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000078487	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10231604	0.84[LWK][hapmap];0.83[YRI][hapmap]
rs1050542	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1141057	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11550034	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12112428	0.90[ASN][1000 genomes]
rs12112642	0.90[ASN][1000 genomes]
rs12534494	0.90[ASN][1000 genomes]
rs12878	0.94[ASW][hapmap];0.84[CEU][hapmap];0.91[LWK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap]
rs13309	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1527423	0.87[MEX][hapmap]
rs1534309	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2272337	0.81[LWK][hapmap]
rs2272338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2285886	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2293481	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34161112	0.84[ASN][1000 genomes]
rs35058708	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35414630	1.00[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs3736590	0.82[LWK][hapmap]
rs3736591	0.94[ASW][hapmap];0.88[LWK][hapmap];0.96[YRI][hapmap]
rs3800951	0.80[LWK][hapmap]
rs3807479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4134888	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4134917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4134923	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4729567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4729568	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4729571	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4729572	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62485010	0.94[ASN][1000 genomes]
rs62485013	0.89[ASN][1000 genomes]
rs6960432	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941290	1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9649220	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs999885	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs999886	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	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
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4729577	ZKSCAN1	cis	multi-tissue	Pritchard
rs4729577	AP4M1	cis	cerebellum	SCAN
rs4729577	AP4M1	cis	Esophagus Muscularis	GTEx
rs4729577	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs4729577	AP4M1	cis	Nerve Tibial	GTEx
rs4729577	ZSCAN21	cis	parietal	SCAN
rs4729577	AP4M1	cis	Stomach	GTEx
rs4729577	AP4M1	cis	Artery Tibial	GTEx
rs4729577	GATS	cis	parietal	SCAN
rs4729577	TAF6	cis	Thyroid	GTEx
rs4729577	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs4729577	MBLAC1	cis	cerebellum	SCAN
rs4729577	SMURF1	cis	cerebellum	SCAN
rs4729577	AP4M1	cis	Adipose Subcutaneous	GTEx
rs4729577	AP4M1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99699800-99703800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr7:99700200-99701800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr7:99700200-99702600	Weak transcription	Primary T cells from cord blood	blood
4	chr7:99700200-99702600	Weak transcription	Liver	Liver
5	chr7:99700200-99702800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr7:99700200-99702800	Weak transcription	Aorta	Aorta
7	chr7:99700200-99703200	Weak transcription	Primary B cells from cord blood	blood
8	chr7:99700200-99703600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:99700200-99709400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:99700200-99716200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:99700200-99716400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr7:99700400-99701800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:99700400-99702400	Weak transcription	Brain Anterior Caudate	brain
14	chr7:99700400-99702600	Weak transcription	Brain Substantia Nigra	brain
15	chr7:99700400-99703400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:99700400-99703400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr7:99700400-99703800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr7:99700400-99703800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr7:99700400-99704400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:99700400-99704400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr7:99700400-99704400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr7:99700400-99705200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr7:99700400-99705800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr7:99700400-99705800	Weak transcription	GM12878-XiMat	blood
25	chr7:99700400-99707000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr7:99700400-99707400	Weak transcription	Fetal Kidney	kidney
27	chr7:99700400-99715800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr7:99700400-99716000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:99700400-99716200	Weak transcription	Psoas Muscle	Psoas
30	chr7:99700400-99716200	Weak transcription	Small Intestine	intestine
31	chr7:99700600-99701800	Weak transcription	Esophagus	oesophagus
32	chr7:99700600-99702400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:99700600-99702600	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr7:99700600-99702800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:99700600-99702800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr7:99700600-99702800	Weak transcription	A549	lung
37	chr7:99700600-99703000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr7:99700600-99703000	Weak transcription	Brain Angular Gyrus	brain
39	chr7:99700600-99703200	Weak transcription	NHEK	skin
40	chr7:99700600-99703400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr7:99700600-99703800	Strong transcription	Colon Smooth Muscle	Colon
42	chr7:99700600-99704200	Weak transcription	HMEC	breast
43	chr7:99700600-99704400	Weak transcription	Fetal Lung	lung
44	chr7:99700600-99705400	Weak transcription	HUVEC	blood vessel
45	chr7:99700600-99706000	Weak transcription	Fetal Heart	heart
46	chr7:99700600-99707400	Weak transcription	Hela-S3	cervix
47	chr7:99700600-99709200	Weak transcription	HepG2	liver
48	chr7:99700600-99710000	Strong transcription	Left Ventricle	heart
49	chr7:99700600-99711000	Weak transcription	Stomach Mucosa	stomach
50	chr7:99700600-99711400	Strong transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links