Variant report

Variant	rs4729532
Chromosome Location	chr7:98978755-98978756
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	POLR2A	chr7:98976820-98979282	GM10847	blood:	n/a	n/a
2	POLR2A	chr7:98976609-98979475	GM12892	blood:	n/a	n/a
3	YY1	chr7:98978431-98979036	GM12891	blood:	n/a	n/a
4	EP300	chr7:98978325-98978811	HepG2	liver:	n/a	n/a
5	MXI1	chr7:98978625-98979968	SK-N-SH	brain:	n/a	chr7:98979641-98979650
6	MAX	chr7:98978472-98979596	HepG2	liver:	n/a	chr7:98979002-98979012 chr7:98978961-98978968
7	RELA	chr7:98977642-98979100	GM12892	blood:	n/a	chr7:98978712-98978721 chr7:98978712-98978721
8	WRNIP1	chr7:98977552-98979294	GM12878	blood:	n/a	n/a
9	PAX5	chr7:98978428-98979034	GM12878	blood:	n/a	n/a
10	BCL3	chr7:98978499-98979094	GM12878	blood:	n/a	chr7:98978711-98978720
11	MYC	chr7:98978723-98979130	HepG2	liver:	n/a	chr7:98979002-98979012 chr7:98978961-98978968
12	MXI1	chr7:98978176-98979613	HepG2	liver:	n/a	n/a
13	BCLAF1	chr7:98976667-98979159	GM12878	blood:	n/a	chr7:98977376-98977389 chr7:98978711-98978720 chr7:98977373-98977386
14	POLR2A	chr7:98976628-98979715	GM15510	blood:	n/a	n/a
15	IRF4	chr7:98977599-98979082	GM12878	blood:	n/a	n/a
16	MAX	chr7:98978131-98979860	HepG2	liver:	n/a	chr7:98979002-98979012 chr7:98978961-98978968 chr7:98978274-98978283
17	POLR2A	chr7:98978734-98979184	A549	lung:	n/a	n/a
18	EBF1	chr7:98977626-98979171	GM12878	blood:	n/a	n/a
19	POLR2A	chr7:98976592-98979794	GM12891	blood:	n/a	n/a
20	ELF1	chr7:98977482-98979107	GM12878	blood:	n/a	chr7:98977917-98977930
21	ATF2	chr7:98977524-98979199	GM12878	blood:	n/a	n/a
22	POU2F2	chr7:98977544-98979203	GM12891	blood:	n/a	n/a
23	POLR2A	chr7:98977475-98979823	K562	blood:	n/a	n/a
24	POLR2A	chr7:98978508-98979207	MCF10A-Er-Src	breast:	n/a	n/a
25	ATF2	chr7:98977541-98979087	GM12878	blood:	n/a	n/a
26	TAF1	chr7:98978458-98978816	GM12892	blood:	n/a	n/a
27	POLR2A	chr7:98976610-98979794	GM18505	blood:	n/a	n/a
28	TAF1	chr7:98978368-98979031	GM12891	blood:	n/a	n/a
29	POLR2A	chr7:98977497-98979791	GM12878	blood:	n/a	n/a
30	POLR2A	chr7:98976834-98979870	Hela-S3	cervix:	n/a	n/a
31	SP1	chr7:98978330-98978769	HepG2	liver:	n/a	chr7:98978554-98978563 chr7:98978420-98978434
32	POLR2A	chr7:98976659-98979619	GM12878	blood:	n/a	n/a
33	STAT5A	chr7:98976702-98980298	GM12878	blood:	n/a	chr7:98979486-98979498 chr7:98979431-98979443
34	SRF	chr7:98978616-98978891	HepG2	liver:	n/a	chr7:98978790-98978801 chr7:98978787-98978801 chr7:98978789-98978802 chr7:98978787-98978805 chr7:98978789-98978800 chr7:98978790-98978804 chr7:98978788-98978803 chr7:98978787-98978804 chr7:98978791-98978805 chr7:98978790-98978807 chr7:98978787-98978805 chr7:98978791-98978800
35	FOXM1	chr7:98976546-98979157	GM12878	blood:	n/a	n/a
36	POLR2A	chr7:98977460-98979044	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr7:98978613-98978765	MCF-7	breast:	n/a	n/a
38	YY1	chr7:98978459-98978976	GM12891	blood:	n/a	n/a
39	YY1	chr7:98977482-98979050	GM12878	blood:	n/a	chr7:98978172-98978180
40	RELA	chr7:98976638-98979173	GM10847	blood:	n/a	chr7:98978712-98978721 chr7:98978712-98978721
41	POLR2A	chr7:98978333-98979724	HepG2	liver:	n/a	n/a
42	MAZ	chr7:98977536-98979069	GM12878	blood:	n/a	chr7:98978961-98978968 chr7:98978274-98978283
43	RELA	chr7:98977622-98979147	GM15510	blood:	n/a	chr7:98978712-98978721 chr7:98978712-98978721
44	POLR2A	chr7:98977666-98979210	PANC-1	pancreas:	n/a	n/a
45	TBL1XR1	chr7:98976750-98979149	GM12878	blood:	n/a	n/a
46	POLR2A	chr7:98978574-98979346	U87	brain:	n/a	n/a
47	RELA	chr7:98977674-98979268	GM19193	blood:	n/a	chr7:98978712-98978721 chr7:98978712-98978721
48	POLR2A	chr7:98976524-98979851	GM12892	blood:	n/a	n/a
49	TCF12	chr7:98978402-98978944	GM12878	blood:	n/a	n/a
50	ELK1	chr7:98977681-98979078	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:98976910..98979073-chr7:98989172..98991412,2	MCF-7	breast:
2	chr7:98975447..98980936-chr7:99003746..99008536,8	MCF-7	breast:
3	chr7:98977788..98980375-chr7:98980403..98983687,6	MCF-7	breast:
4	chr7:98977857..98980973-chr7:99035179..99039094,4	MCF-7	breast:
5	chr7:98975439..98979350-chr7:99003635..99008025,5	K562	blood:
6	chr7:98978155..98981581-chr7:99004279..99007902,6	MCF-7	breast:
7	chr7:98966478..98969149-chr7:98977868..98979453,2	MCF-7	breast:
8	chr7:98978195..98983060-chr7:98988487..98993755,6	MCF-7	breast:

Variant related genes	Relation type
ARPC1B	TF binding region
ENSG00000106245	Chromatin interaction
ENSG00000130429	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000160917	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10155966	0.92[ASW][hapmap];0.91[CEU][hapmap];0.81[MKK][hapmap];0.80[EUR][1000 genomes]
rs10225529	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10238965	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs10243678	0.92[ASW][hapmap];0.91[CEU][hapmap];0.81[MKK][hapmap]
rs10258757	0.92[ASW][hapmap];0.91[CEU][hapmap];0.83[MKK][hapmap]
rs10270459	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs10270917	0.91[CEU][hapmap]
rs10271049	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs10272998	0.83[ASW][hapmap];0.91[CEU][hapmap]
rs10277149	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10279308	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1043466	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs10953288	0.80[CEU][hapmap]
rs11762273	0.92[ASW][hapmap];0.91[CEU][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs11771702	0.91[CEU][hapmap]
rs11976018	0.83[ASW][hapmap];0.84[CEU][hapmap];0.81[MKK][hapmap]
rs11978089	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12112936	0.91[CEU][hapmap]
rs12113440	0.91[CEU][hapmap]
rs12538893	0.81[CEU][hapmap]
rs17161662	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs17161669	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs17161695	0.91[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1980307	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs2003499	1.00[CEU][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2057906	0.85[YRI][hapmap]
rs2072181	0.92[ASW][hapmap];0.91[CEU][hapmap]
rs2240384	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs2272168	0.84[CEU][hapmap]
rs2280600	0.84[CEU][hapmap]
rs2280601	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs2286162	0.91[CEU][hapmap]
rs3137	0.84[CEU][hapmap]
rs3801288	0.91[CEU][hapmap]
rs6943920	0.91[ASW][hapmap];0.91[CEU][hapmap];0.81[MKK][hapmap]
rs6955490	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6957987	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs6962772	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs733991	0.91[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs7794705	0.84[CEU][hapmap]
rs883403	0.84[CEU][hapmap]
rs917154	0.83[ASW][hapmap];0.83[CEU][hapmap];0.81[MKK][hapmap]
rs9969217	0.82[GIH][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS 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 miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4729532	CPSF4	cis	parietal	SCAN
rs4729532	GATS	cis	parietal	SCAN
rs4729532	PILRB	cis	lymphoblastoid	GTEx
rs4729532	STAG3	cis	cerebellum	SCAN
rs4729532	OR2AE1	cis	parietal	SCAN
rs4729532	ZKSCAN1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98971000-98990400	Weak transcription	Fetal Kidney	kidney
2	chr7:98973200-98978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:98973400-98978800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:98973400-98979000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:98973400-98979200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr7:98973400-98984000	Weak transcription	Aorta	Aorta
7	chr7:98973400-98984200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:98973400-98984200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:98973400-98984200	Weak transcription	Ovary	ovary
10	chr7:98973400-98984400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:98973400-98987400	Weak transcription	Brain Germinal Matrix	brain
12	chr7:98973400-98987800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:98973400-98989800	Weak transcription	Brain Angular Gyrus	brain
14	chr7:98974800-98979800	Strong transcription	Fetal Intestine Small	intestine
15	chr7:98976600-98978800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:98976600-98978800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr7:98976600-98978800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr7:98976600-98979000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr7:98976600-98979200	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr7:98976600-98979200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:98976600-98979200	Flanking Active TSS	GM12878-XiMat	blood
22	chr7:98976600-98979400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:98976800-98979000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr7:98976800-98979000	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr7:98976800-98979000	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr7:98976800-98979000	Enhancers	Stomach Mucosa	stomach
27	chr7:98976800-98979200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr7:98976800-98979200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr7:98976800-98979400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr7:98976800-98979400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr7:98976800-98979800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:98977000-98978800	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr7:98977000-98978800	Flanking Active TSS	Colon Smooth Muscle	Colon
34	chr7:98977000-98979200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr7:98977000-98979200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr7:98977000-98979400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr7:98977000-98979600	Genic enhancers	Muscle Satellite Cultured Cells	--
38	chr7:98977000-98979600	Enhancers	Esophagus	oesophagus
39	chr7:98977000-98979800	Enhancers	Fetal Muscle Trunk	muscle
40	chr7:98977200-98978800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr7:98977200-98978800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr7:98977200-98978800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:98977200-98979200	Enhancers	Brain Cingulate Gyrus	brain
44	chr7:98977200-98979800	Enhancers	Left Ventricle	heart
45	chr7:98977400-98978800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr7:98977600-98978800	Enhancers	Brain Substantia Nigra	brain
47	chr7:98977600-98979000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr7:98977600-98979200	Transcr. at gene 5' and 3'	Dnd41	blood
49	chr7:98977600-98979400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr7:98977600-98979400	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum

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