Variant report

Variant	rs479407
Chromosome Location	chr1:10673194-10673195
allele	C/T
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:8)
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	MXI1	chr1:10672087-10673408	SK-N-SH	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10672111..10674098-chr1:10684480..10687476,2	K562	blood:
2	chr1:10672897..10674878-chr1:10677717..10679649,2	K562	blood:
3	chr1:10672064..10673833-chr1:10681009..10682512,2	MCF-7	breast:
4	chr1:10660994..10662819-chr1:10672877..10674631,2	K562	blood:
5	chr1:10673034..10676148-chr1:10680222..10683024,3	K562	blood:
6	chr1:10656580..10658431-chr1:10672965..10675742,2	K562	blood:
7	chr1:10666567..10669351-chr1:10671617..10674178,2	K562	blood:
8	chr1:10662635..10666770-chr1:10672476..10675391,3	K562	blood:

No data

Variant related genes	Relation type
RN7SL614P	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17035406	0.85[YRI][hapmap]
rs284269	0.84[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs284271	0.88[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes]
rs284281	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs517344	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1010424	chr1:10667559-10747891	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv464394	chr1:10673094-10767902	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv545396	chr1:10673094-10767902	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv1828181	chr1:10673130-10829937	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv464505	chr1:10673194-10767785	Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv545397	chr1:10673194-10767785	Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv464616	chr1:10673194-10767902	Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv545398	chr1:10673194-10767902	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv464727	chr1:10673194-10777260	Bivalent Enhancer ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv545399	chr1:10673194-10777260	Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10632600-10698000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:10644200-10683400	Weak transcription	K562	blood
3	chr1:10651600-10715800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:10652400-10678400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:10653600-10688600	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:10654800-10691600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:10655800-10677200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:10656200-10675000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:10656400-10675000	Weak transcription	GM12878-XiMat	blood
10	chr1:10656800-10687200	Weak transcription	Small Intestine	intestine
11	chr1:10657600-10675400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:10657600-10683200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:10657800-10683600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr1:10657800-10684200	Weak transcription	Colonic Mucosa	Colon
15	chr1:10658000-10674600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:10658200-10694400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:10658400-10674600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:10658400-10674800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:10658400-10675600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:10658400-10678200	Weak transcription	Ovary	ovary
21	chr1:10658400-10688600	Weak transcription	Fetal Lung	lung
22	chr1:10658400-10691600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:10658600-10674000	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:10658600-10675600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:10658600-10678000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:10658800-10678400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:10659200-10687800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:10659400-10673800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:10659400-10684400	Weak transcription	Dnd41	blood
30	chr1:10659600-10678400	Weak transcription	Placenta	Placenta
31	chr1:10659600-10683800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:10659800-10674600	Weak transcription	Brain Anterior Caudate	brain
33	chr1:10659800-10676200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:10659800-10690800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr1:10660000-10674800	Weak transcription	Brain Germinal Matrix	brain
36	chr1:10660000-10682000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:10660000-10683600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:10660000-10684200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:10660200-10684400	Weak transcription	NHLF	lung
40	chr1:10660200-10697600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:10660400-10679000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:10660400-10679000	Weak transcription	HMEC	breast
43	chr1:10660400-10683800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:10661800-10675600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:10661800-10678200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:10661800-10678400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:10661800-10692000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:10662000-10674600	Weak transcription	Brain Substantia Nigra	brain
49	chr1:10662000-10675600	Weak transcription	Esophagus	oesophagus
50	chr1:10662000-10676600	Weak transcription	Adipose Nuclei	Adipose

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