Variant report

Variant	rs12781700
Chromosome Location	chr10:5936425-5936426
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	POLR2A	chr10:5936364-5940412	K562	blood:	n/a	n/a
2	POLR2A	chr10:5936329-5937299	K562	blood:	n/a	n/a
3	CEBPB	chr10:5936290-5937248	K562	blood:	n/a	chr10:5936679-5936692
4	TEAD4	chr10:5936415-5937318	K562	blood:	n/a	n/a
5	MAX	chr10:5936379-5936785	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:5935195..5937102-chr10:6243588..6245241,2	MCF-7	breast:
2	chr10:5726920..5728949-chr10:5933520..5936437,2	K562	blood:
3	chr10:5934107..5937505-chr10:5944279..5947723,3	K562	blood:
4	chr10:5852308..5856409-chr10:5935538..5939554,4	K562	blood:
5	chr10:5853439..5857708-chr10:5926443..5936823,24	K562	blood:

Variant related genes	Relation type
ANKRD16	TF binding region
ENSG00000213994	Chromatin interaction
ENSG00000057608	Chromatin interaction
ENSG00000170525	Chromatin interaction
ENSG00000108021	Chromatin interaction
ENSG00000134452	Chromatin interaction
ENSG00000272764	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10508298	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508299	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255698	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255774	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255780	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255971	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255974	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256009	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360409	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12767690	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774228	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774886	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12785055	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17319759	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976655	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985072	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2387092	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36049919	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56369297	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61832959	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6602330	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7067928	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082434	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090411	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893735	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7919913	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv825229	chr10:5886905-5967697	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv466724	chr10:5920836-5938544	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
7	nsv549906	chr10:5920836-5938544	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5933200-5948200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:5933200-5949800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr10:5933200-5977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr10:5933400-5936600	Weak transcription	HSMMtube	muscle
5	chr10:5933400-5938800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr10:5933400-5948200	Weak transcription	Ovary	ovary
7	chr10:5933400-5948400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr10:5933400-5949800	Weak transcription	Fetal Brain Male	brain
9	chr10:5933600-5937000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr10:5933600-5948200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr10:5933600-5951600	Weak transcription	Stomach Mucosa	stomach
12	chr10:5933800-5939200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr10:5933800-5941200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr10:5934000-5939800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr10:5934200-5937800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr10:5934200-5938600	Strong transcription	Fetal Intestine Large	intestine
17	chr10:5934200-5939400	Strong transcription	Fetal Muscle Leg	muscle
18	chr10:5934400-5937600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr10:5934400-5938000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr10:5934600-5937400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr10:5934600-5941000	Strong transcription	NHEK	skin
22	chr10:5934800-5940200	Weak transcription	Colon Smooth Muscle	Colon
23	chr10:5934800-5948000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr10:5935000-5937200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr10:5935000-5938000	Strong transcription	Dnd41	blood
26	chr10:5935200-5937600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr10:5935200-5941800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr10:5935200-5947400	Weak transcription	Small Intestine	intestine
29	chr10:5935400-5936800	Strong transcription	Primary B cells from cord blood	blood
30	chr10:5935400-5937000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr10:5935400-5937200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr10:5935400-5937800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr10:5935400-5937800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr10:5935400-5938000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr10:5935400-5938000	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr10:5935400-5938600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr10:5935400-5939200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr10:5935400-5939800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr10:5935400-5940400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr10:5935400-5941200	Strong transcription	Fetal Lung	lung
41	chr10:5935600-5937600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr10:5935600-5938200	Strong transcription	NH-A	brain
43	chr10:5935600-5938400	Strong transcription	HepG2	liver
44	chr10:5935600-5938600	Strong transcription	Primary hematopoietic stem cells	blood
45	chr10:5935600-5939000	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr10:5935600-5939400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr10:5935600-5940200	Strong transcription	Placenta	Placenta
48	chr10:5935600-5943000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr10:5935600-5962000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr10:5935800-5937000	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links