Variant report

Variant	rs3865000
Chromosome Location	chr13:39609603-39609604
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	E2F4	chr13:39609410-39609637	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr13:39609476-39609632	K562	blood:	n/a	n/a
3	NRF1	chr13:39609274-39609631	H1-hESC	embryonic stem cell:	n/a	n/a
4	KAP1	chr13:39609332-39610079	HEK293	kidney:	n/a	n/a
5	POLR2A	chr13:39609591-39609741	H1-hESC	embryonic stem cell:	n/a	n/a
6	GATA1	chr13:39608902-39610135	PBDE	blood:	n/a	n/a
7	SIN3A	chr13:39609383-39609805	H1-hESC	embryonic stem cell:	n/a	n/a
8	MYC	chr13:39609509-39611304	MCF10A-Er-Src	breast:	n/a	chr13:39610504-39610514 chr13:39610831-39610839
9	MYC	chr13:39609367-39610703	MCF10A-Er-Src	breast:	n/a	chr13:39610504-39610514
10	MAZ	chr13:39609333-39609649	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:39608105..39609639-chr13:40260400..40262356,2	K562	blood:

Variant related genes	Relation type
PROSER1	TF binding region
NHLRC3	TF binding region
ENSG00000133103	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11840611	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12430086	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1326404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409442	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536342	0.93[EUR][1000 genomes]
rs1853970	0.87[EUR][1000 genomes]
rs1887111	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1926474	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2094251	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2148418	0.87[EUR][1000 genomes]
rs2324160	0.86[EUR][1000 genomes]
rs3751376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563660	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs6563661	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs6563662	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs6563663	0.87[ASN][1000 genomes]
rs71439792	0.84[EUR][1000 genomes]
rs7320516	0.88[EUR][1000 genomes]
rs7324256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7324837	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7325996	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7489497	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985641	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs9315647	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9315650	0.93[EUR][1000 genomes]
rs9566395	0.86[EUR][1000 genomes]
rs9576680	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9576687	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576723	0.88[EUR][1000 genomes]
rs9603503	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9888511	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2753642	chr13:39522300-39649000	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2753553	chr13:39526600-39649000	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39588600-39610400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:39599800-39610400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:39599800-39610600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:39599800-39611200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:39600600-39610600	Weak transcription	Lung	lung
6	chr13:39607200-39610000	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr13:39608400-39609800	Enhancers	Fetal Thymus	thymus
8	chr13:39608400-39610000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr13:39608400-39610000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr13:39608400-39610000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr13:39608400-39610400	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr13:39608400-39610400	Enhancers	Primary B cells from peripheral blood	blood
13	chr13:39608600-39610000	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr13:39608600-39610200	Flanking Active TSS	Dnd41	blood
15	chr13:39608600-39610800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr13:39608800-39609800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr13:39608800-39609800	Flanking Active TSS	Fetal Brain Female	brain
18	chr13:39608800-39609800	Flanking Active TSS	HepG2	liver
19	chr13:39608800-39610000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr13:39608800-39610000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr13:39608800-39610200	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr13:39608800-39610200	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr13:39608800-39610400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr13:39608800-39610400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr13:39608800-39611200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr13:39609000-39609800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:39609000-39609800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr13:39609000-39610400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr13:39609000-39610400	Enhancers	Fetal Brain Male	brain
30	chr13:39609000-39611400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr13:39609000-39615000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr13:39609000-39615200	Active TSS	K562	blood
33	chr13:39609200-39609800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr13:39609200-39610000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr13:39609200-39610200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr13:39609200-39610400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr13:39609200-39610600	Weak transcription	Small Intestine	intestine
38	chr13:39609200-39613600	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr13:39609200-39613800	Active TSS	GM12878-XiMat	blood
40	chr13:39609400-39609800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
41	chr13:39609400-39609800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr13:39609400-39609800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr13:39609400-39609800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr13:39609400-39609800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr13:39609400-39609800	Flanking Active TSS	Brain Angular Gyrus	brain
46	chr13:39609400-39609800	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr13:39609400-39609800	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr13:39609400-39609800	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr13:39609400-39609800	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr13:39609400-39609800	Flanking Active TSS	Fetal Kidney	kidney

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