Variant report

Variant	rs10007915
Chromosome Location	chr4:106065308-106065309
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:106065283-106065479	MCF-7	breast:	n/a	n/a

No data

(count:14 , 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	chr4:105812145..105831361-chr4:106062414..106073665,101	MCF-7	breast:
5	chr4:106064996..106066911-chr4:106094285..106096371,2	MCF-7	breast:
6	chr4:106064096..106067013-chr4:106110754..106112380,2	MCF-7	breast:
7	chr4:106064984..106068563-chr4:106391196..106395238,6	K562	blood:
8	chr4:106022079..106026589-chr4:106064672..106069140,4	MCF-7	breast:
9	chr4:105883010..105897017-chr4:106062943..106072055,55	MCF-7	breast:
10	chr4:106064280..106066149-chr4:106628359..106630595,2	MCF-7	breast:
11	chr18:10679396..10682032-chr4:106065086..106068050,2	MCF-7	breast:
12	chr4:105884036..105898505-chr4:106054854..106072562,138	MCF-7	breast:
13	chr4:106064646..106070521-chr4:106098298..106104512,9	MCF-7	breast:
14	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
ENSG00000138777	Chromatin interaction
ENSG00000251473	Chromatin interaction
ENSG00000138780	Chromatin interaction
ENSG00000248373	Chromatin interaction
ENSG00000154864	Chromatin interaction
ENSG00000168769	Chromatin interaction
ENSG00000248242	Chromatin interaction
ENSG00000251906	Chromatin interaction
ENSG00000138785	Chromatin interaction
ENSG00000251586	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11735256	0.89[GIH][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs1541374	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2007403	0.86[GIH][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes]
rs2047409	0.80[AMR][1000 genomes]
rs4698932	0.90[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.98[ASN][1000 genomes]
rs6533183	0.89[GIH][hapmap];0.87[TSI][hapmap]
rs6839705	0.91[GIH][hapmap];0.85[TSI][hapmap]
rs7661349	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7679673	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][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	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
rs10007915	CXXC4	cis	cerebellum	SCAN
rs10007915	OSTC	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106059400-106065600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr4:106061800-106067000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:106062200-106067000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:106062400-106066200	Weak transcription	Fetal Lung	lung
5	chr4:106062400-106066400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:106062400-106066400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:106062400-106066600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:106062400-106066600	Weak transcription	Osteobl	bone
9	chr4:106062400-106066800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:106062400-106066800	Weak transcription	HMEC	breast
11	chr4:106062600-106066200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:106062600-106066200	Weak transcription	HepG2	liver
13	chr4:106062600-106066600	Weak transcription	NHEK	skin
14	chr4:106062600-106066800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:106062800-106066200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr4:106064000-106066600	Weak transcription	HUVEC	blood vessel
17	chr4:106064200-106065600	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr4:106064400-106066200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr4:106064600-106065400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr4:106064600-106066000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:106064600-106066200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:106064800-106065600	Weak transcription	Primary B cells from cord blood	blood
23	chr4:106064800-106066400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr4:106064800-106071800	Active TSS	GM12878-XiMat	blood
25	chr4:106065000-106066800	Weak transcription	Colonic Mucosa	Colon
26	chr4:106065200-106065400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:106065200-106065400	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr4:106065200-106066200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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