Variant report

Variant	rs17035311
Chromosome Location	chr4:106066293-106066294
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr4:106066251-106067175	GM12878	blood:	n/a	n/a
2	ATF2	chr4:106066253-106066940	GM12878	blood:	n/a	n/a
3	SPI1	chr4:106066120-106066623	HL-60	blood:	n/a	n/a
4	SPI1	chr4:106066279-106066429	K562	blood:	n/a	n/a
5	PML	chr4:106066139-106069518	GM12878	blood:	n/a	n/a
6	POLR2A	chr4:106066154-106067028	HL-60	blood:	n/a	n/a
7	SPI1	chr4:106066235-106066519	GM12891	blood:	n/a	n/a
8	SPI1	chr4:106066186-106066524	GM12878	blood:	n/a	n/a
9	SPI1	chr4:106066269-106066521	GM12891	blood:	n/a	n/a
10	RUNX3	chr4:106066242-106067720	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:106066287-106069785	GM12891	blood:	n/a	n/a
12	NFIC	chr4:106066160-106067611	GM12878	blood:	n/a	n/a
13	REST	chr4:106066219-106066953	HL-60	blood:	n/a	n/a
14	SPI1	chr4:106066096-106066687	HL-60	blood:	n/a	n/a
15	POLR2A	chr4:106065596-106069239	MCF-7	breast:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:106064287..106066439-chr4:106394803..106396308,2	MCF-7	breast:
2	chr4:106064811..106067302-chr4:106067349..106069355,2	K562	blood:
3	chr4:105778129..105779689-chr4:106064398..106066693,2	MCF-7	breast:
4	chr4:105985714..105987494-chr4:106065322..106066910,2	MCF-7	breast:
5	chr4:105812145..105831361-chr4:106062414..106073665,101	MCF-7	breast:
6	chr4:106064996..106066911-chr4:106094285..106096371,2	MCF-7	breast:
7	chr4:106026817..106029073-chr4:106065423..106067037,2	MCF-7	breast:
8	chr4:106064096..106067013-chr4:106110754..106112380,2	MCF-7	breast:
9	chr10:5539087..5542053-chr4:106066148..106068545,2	MCF-7	breast:
10	chr4:106064984..106068563-chr4:106391196..106395238,6	K562	blood:
11	chr4:106022079..106026589-chr4:106064672..106069140,4	MCF-7	breast:
12	chr4:105883010..105897017-chr4:106062943..106072055,55	MCF-7	breast:
13	chr18:10679396..10682032-chr4:106065086..106068050,2	MCF-7	breast:
14	chr4:105884036..105898505-chr4:106054854..106072562,138	MCF-7	breast:
15	chr17:60554571..60556757-chr4:106065577..106067920,2	MCF-7	breast:
16	chr4:106064646..106070521-chr4:106098298..106104512,9	MCF-7	breast:
17	chr4:105823235..105830393-chr4:106065333..106069817,8	MCF-7	breast:
18	chr4:106063836..106066405-chr4:106394011..106395544,2	MCF-7	breast:

No data

Variant related genes	Relation type
TET2	TF binding region
ENSG00000251259	TF binding region
ENSG00000146872	Chromatin interaction
ENSG00000251906	Chromatin interaction
ENSG00000251473	Chromatin interaction
ENSG00000178372	Chromatin interaction
ENSG00000248242	Chromatin interaction
ENSG00000252136	Chromatin interaction
ENSG00000154864	Chromatin interaction
ENSG00000251586	Chromatin interaction
ENSG00000168769	Chromatin interaction
ENSG00000138777	Chromatin interaction
ENSG00000248373	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10488913	1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11097881	0.82[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11728350	0.92[CEU][hapmap]
rs11729069	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17035289	1.00[ASW][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17035310	0.93[CEU][hapmap]
rs17616993	0.82[ASN][1000 genomes]
rs6825684	0.93[CEU][hapmap]
rs6843555	0.94[ASN][1000 genomes]
rs763480	0.93[CEU][hapmap]

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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17035311	BDH2	cis	cerebellum	SCAN
rs17035311	CXXC4	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106061800-106067000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:106062200-106067000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:106062400-106066400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:106062400-106066400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:106062400-106066600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:106062400-106066600	Weak transcription	Osteobl	bone
7	chr4:106062400-106066800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:106062400-106066800	Weak transcription	HMEC	breast
9	chr4:106062600-106066600	Weak transcription	NHEK	skin
10	chr4:106062600-106066800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:106064000-106066600	Weak transcription	HUVEC	blood vessel
12	chr4:106064800-106066400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr4:106064800-106071800	Active TSS	GM12878-XiMat	blood
14	chr4:106065000-106066800	Weak transcription	Colonic Mucosa	Colon
15	chr4:106065400-106066600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr4:106065400-106066800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:106065400-106067000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:106065600-106066400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr4:106065600-106066600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:106065800-106066800	Weak transcription	Psoas Muscle	Psoas
21	chr4:106065800-106067000	Weak transcription	Small Intestine	intestine
22	chr4:106066000-106066400	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr4:106066000-106067600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:106066200-106066400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr4:106066200-106066400	Enhancers	Fetal Lung	lung
26	chr4:106066200-106066400	Enhancers	A549	lung
27	chr4:106066200-106066600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
28	chr4:106066200-106066600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr4:106066200-106066600	Enhancers	Primary B cells from peripheral blood	blood
30	chr4:106066200-106066600	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr4:106066200-106066600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:106066200-106066600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr4:106066200-106066600	Enhancers	HepG2	liver
34	chr4:106066200-106066800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:106066200-106066800	Active TSS	Adipose Nuclei	Adipose
36	chr4:106066200-106067000	Active TSS	Placenta	Placenta
37	chr4:106066200-106067400	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr4:106066200-106067400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr4:106066200-106070000	Active TSS	Monocytes-CD14+_RO01746	blood
40	chr4:106066200-106070200	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr4:106066200-106070600	Active TSS	Primary monocytes fromperipheralblood	blood
42	chr4:106066200-106070800	Active TSS	Duodenum Smooth Muscle	Duodenum

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