Variant report

Variant	rs3847018
Chromosome Location	chr7:39993262-39993263
allele	C/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	TEAD4	chr7:39993245-39993575	H1-hESC	embryonic stem cell:	n/a	n/a
2	KAP1	chr7:39992776-39993757	K562	blood:	n/a	n/a
3	POLR2A	chr7:39990966-39993370	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr7:39991082-39993478	Hela-S3	cervix:	n/a	chr7:39992576-39992587 chr7:39992576-39992589 chr7:39992971-39992982
5	FOXA2	chr7:39993192-39993441	HepG2	liver:	n/a	n/a
6	ZNF143	chr7:39993091-39993433	K562	blood:	n/a	n/a
7	USF2	chr7:39993083-39993567	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr7:39987858-39993456	GM12878	blood:	n/a	n/a
9	FOXA1	chr7:39993172-39993472	HepG2	liver:	n/a	n/a
10	MXI1	chr7:39993248-39993736	GM12878	blood:	n/a	n/a
11	RCOR1	chr7:39993146-39993556	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr7:39987517-39993787	SK-N-SH	brain:	n/a	n/a
13	ZNF143	chr7:39993182-39993411	Hela-S3	cervix:	n/a	n/a
14	FOXA1	chr7:39993091-39993493	HepG2	liver:	n/a	n/a
15	SIN3A	chr7:39993246-39993531	H1-hESC	embryonic stem cell:	n/a	n/a
16	FOXA1	chr7:39993207-39993473	HepG2	liver:	n/a	n/a
17	UBTF	chr7:39993161-39993441	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:39992254..39999333-chr7:39999543..40002599,8	K562	blood:
2	chr7:39992705..39994767-chr7:40040920..40043283,2	K562	blood:
3	chr7:39992179..39995720-chr7:40011134..40014847,3	K562	blood:
4	chr7:39991743..39994324-chr7:40009939..40012634,2	K562	blood:

Variant related genes	Relation type
ENSG00000259826	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10234693	0.91[YRI][hapmap]
rs10246466	0.82[YRI][hapmap]
rs1082028	0.83[AFR][1000 genomes]
rs1082030	0.86[AFR][1000 genomes]
rs11771104	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1257699	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs1267260	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17171658	0.82[YRI][hapmap]
rs2052097	0.82[YRI][hapmap]
rs4723924	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6952597	0.82[YRI][hapmap]
rs6970705	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6970838	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6974493	0.82[YRI][hapmap]
rs6978474	0.80[YRI][hapmap]
rs773381	0.87[AFR][1000 genomes]
rs773385	0.87[AFR][1000 genomes]
rs773386	0.87[AFR][1000 genomes]
rs773403	0.85[AFR][1000 genomes]
rs773414	0.87[AFR][1000 genomes]
rs773415	0.87[AFR][1000 genomes]
rs773424	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs7797041	0.82[YRI][hapmap]
rs7799846	0.82[YRI][hapmap]
rs798855	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798856	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs798858	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs798861	0.80[AFR][1000 genomes];0.91[EUR][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	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv887976	chr7:39874986-40018693	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv887977	chr7:39885541-40018693	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3847018	CDC2L5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39987800-39993400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:39988000-39993400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:39988000-39993400	Active TSS	Osteobl	bone
4	chr7:39988000-39993600	Active TSS	Colonic Mucosa	Colon
5	chr7:39988000-39993800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr7:39988000-39993800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr7:39988000-39994000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr7:39988200-39993400	Active TSS	Aorta	Aorta
9	chr7:39988200-39993400	Active TSS	Psoas Muscle	Psoas
10	chr7:39988200-39993400	Active TSS	Right Ventricle	heart
11	chr7:39988200-39993600	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr7:39988200-39993800	Active TSS	H1 Cell Line	embryonic stem cell
13	chr7:39988200-39996200	Active TSS	GM12878-XiMat	blood
14	chr7:39988400-39993400	Active TSS	Primary T cells fromperipheralblood	blood
15	chr7:39988400-39993800	Active TSS	HSMMtube	muscle
16	chr7:39988400-39994200	Active TSS	NHLF	lung
17	chr7:39990200-39993600	Active TSS	Stomach Smooth Muscle	stomach
18	chr7:39991000-39993600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr7:39991000-39993600	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr7:39991200-39993600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:39991400-39993600	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr7:39991400-39993800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr7:39991400-39993800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr7:39991400-39994200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr7:39991400-39994200	Active TSS	Right Atrium	heart
26	chr7:39991400-39994600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:39991600-39993600	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr7:39991600-39993600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr7:39991600-39993600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:39991600-39993600	Flanking Active TSS	Liver	Liver
31	chr7:39991600-39993800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr7:39991600-39994000	Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr7:39991600-39994400	Weak transcription	Spleen	Spleen
34	chr7:39991800-39994400	Weak transcription	Pancreas	Pancrea
35	chr7:39991800-39994600	Weak transcription	Gastric	stomach
36	chr7:39991800-39996200	Weak transcription	Esophagus	oesophagus
37	chr7:39991800-40000200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:39991800-40000800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr7:39991800-40005200	Weak transcription	Lung	lung
40	chr7:39992000-39993400	Weak transcription	Stomach Mucosa	stomach
41	chr7:39992000-39993800	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr7:39992000-39994000	Active TSS	HepG2	liver
43	chr7:39992000-39994800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr7:39992000-39999200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr7:39992000-40006400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr7:39992400-39993600	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr7:39992400-39993600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr7:39992400-39993800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr7:39992400-39993800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr7:39992400-39993800	Flanking Active TSS	HUVEC	blood vessel

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