Variant report

Variant	rs1045012
Chromosome Location	chr7:98984354-98984355
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:98984148-98984519	MCF-7	breast:	n/a	n/a
2	CTCF	chr7:98984085-98984997	A549	lung:	n/a	n/a
3	BCL3	chr7:98984143-98984671	A549	lung:	n/a	n/a
4	POLR2A	chr7:98983899-98984691	GM12878	blood:	n/a	n/a
5	STAT5A	chr7:98984028-98984824	GM12878	blood:	n/a	n/a
6	CTCF	chr7:98984280-98984430	RPTEC	kidney:	n/a	n/a
7	POLR2A	chr7:98983914-98984655	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr7:98984183-98984936	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr7:98983953-98984618	GM12892	blood:	n/a	n/a
10	POLR2A	chr7:98983915-98984863	HL-60	blood:	n/a	n/a
11	POLR2A	chr7:98983952-98985267	GM12891	blood:	n/a	n/a
12	POLR2A	chr7:98984198-98984754	GM12891	blood:	n/a	n/a
13	POLR2A	chr7:98984258-98984576	A549	lung:	n/a	n/a
14	POLR2A	chr7:98984022-98984383	GM12892	blood:	n/a	n/a
15	POLR2A	chr7:98983906-98984870	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr7:98984001-98984761	GM12878	blood:	n/a	n/a
17	POLR2A	chr7:98984331-98984644	HCT-116	colon:	n/a	n/a
18	POLR2A	chr7:98983958-98984668	GM18505	blood:	n/a	n/a
19	POLR2A	chr7:98984033-98984647	HepG2	liver:	n/a	n/a
20	POLR2A	chr7:98983917-98984830	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr7:98984114-98984650	GM12891	blood:	n/a	n/a
22	POLR2A	chr7:98983818-98984912	K562	blood:	n/a	n/a
23	POLR2A	chr7:98983893-98984632	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr7:98984345-98984509	A549	lung:	n/a	n/a
25	POLR2A	chr7:98983912-98984928	GM12878	blood:	n/a	n/a
26	PML	chr7:98984102-98984766	GM12878	blood:	n/a	n/a
27	POLR2A	chr7:98984209-98985606	HepG2	liver:	n/a	n/a
28	POLR2A	chr7:98984235-98984935	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr7:98984282-98984553	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr7:98983966-98984965	K562	blood:	n/a	n/a
31	POLR2A	chr7:98983835-98984687	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr7:98983966-98985018	K562	blood:	n/a	n/a
33	POLR2A	chr7:98983940-98984537	GM12878	blood:	n/a	n/a
34	POLR2A	chr7:98984313-98984474	A549	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:98970993..98974296-chr7:98982055..98984760,3	K562	blood:
2	chr7:98960796..98963310-chr7:98983560..98985753,2	MCF-7	breast:
3	chr7:98981776..98988825-chr7:99001775..99008244,9	K562	blood:

No data

Variant related genes	Relation type
ARPC1B	TF binding region
ENSG00000106245	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000130429	Chromatin interaction
ENSG00000241685	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10251282	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10279308	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11972210	0.83[ASN][1000 genomes]
rs11978089	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17161700	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17161726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17854665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2003499	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2293256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404487	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404488	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28377312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28460612	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28558950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28668326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28753399	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34943973	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3528	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3823813	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41385645	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs45441991	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45448997	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45451992	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45461000	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45492501	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45529541	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45555335	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45592335	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55927283	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55942267	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56167514	0.94[ASN][1000 genomes]
rs57367781	0.94[ASN][1000 genomes]
rs57832867	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59240302	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59672032	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955490	1.00[JPT][hapmap]
rs6974831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs73397447	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73397481	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73397499	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401507	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401510	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401516	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403247	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73403272	0.94[ASN][1000 genomes]
rs73403286	0.94[ASN][1000 genomes]
rs73403290	0.94[ASN][1000 genomes]
rs73405247	0.94[ASN][1000 genomes]
rs73711280	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711293	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73711294	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73713507	0.94[ASN][1000 genomes]
rs7794068	0.94[ASN][1000 genomes]
rs7805661	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs917152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952319	1.00[JPT][hapmap];0.89[ASN][1000 genomes]

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

No data

Chromatin state (count:123 , 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	chr7:98973400-98984400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr7:98973400-98987400	Weak transcription	Brain Germinal Matrix	brain
4	chr7:98973400-98987800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:98973400-98989800	Weak transcription	Brain Angular Gyrus	brain
6	chr7:98978000-98987000	Weak transcription	Small Intestine	intestine
7	chr7:98978200-98989800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:98978600-98984400	Weak transcription	NH-A	brain
9	chr7:98978800-98985000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:98978800-98989000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:98979000-98984600	Genic enhancers	Primary monocytes fromperipheralblood	blood
12	chr7:98979000-98989600	Weak transcription	Stomach Mucosa	stomach
13	chr7:98979200-98984400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr7:98979200-98987000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:98979200-98987000	Weak transcription	HSMM	muscle
16	chr7:98979200-98989600	Weak transcription	Brain Substantia Nigra	brain
17	chr7:98979400-98984600	Genic enhancers	Monocytes-CD14+_RO01746	blood
18	chr7:98979400-99001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr7:98979600-98989800	Weak transcription	Fetal Heart	heart
20	chr7:98979600-98990200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:98979600-98990200	Weak transcription	Right Atrium	heart
22	chr7:98980000-98984400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr7:98980400-99003800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr7:98980600-98989600	Strong transcription	NHEK	skin
25	chr7:98980800-98990000	Strong transcription	NHLF	lung
26	chr7:98980800-99000600	Strong transcription	Dnd41	blood
27	chr7:98981000-98988400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr7:98981000-98993000	Strong transcription	A549	lung
29	chr7:98981200-98989800	Strong transcription	Fetal Intestine Small	intestine
30	chr7:98981200-98989800	Strong transcription	Thymus	Thymus
31	chr7:98981200-98990000	Strong transcription	K562	blood
32	chr7:98981400-98989800	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr7:98981400-98989800	Strong transcription	Fetal Stomach	stomach
34	chr7:98981600-98989800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:98981800-98986800	Weak transcription	Fetal Brain Female	brain
36	chr7:98981800-98988800	Strong transcription	GM12878-XiMat	blood
37	chr7:98981800-98989800	Weak transcription	Fetal Brain Male	brain
38	chr7:98982200-98984400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr7:98982400-98987200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr7:98982400-98987400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr7:98982400-98989600	Strong transcription	Spleen	Spleen
42	chr7:98982400-98989800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr7:98982800-98989000	Strong transcription	Fetal Thymus	thymus
44	chr7:98983000-98984400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr7:98983000-98984600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:98983000-98984800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr7:98983000-98988600	Strong transcription	Gastric	stomach
48	chr7:98983000-98989400	Strong transcription	Fetal Muscle Leg	muscle
49	chr7:98983000-98989600	Strong transcription	HMEC	breast
50	chr7:98983000-98989600	Strong transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links