Variant report

Variant	rs10040696
Chromosome Location	chr5:108242804-108242805
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:32696969..32699355-chr5:108240635..108243307,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10079165	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2081130	0.83[ASN][1000 genomes]
rs4604227	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6594340	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6875320	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7700630	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7731891	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9885082	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[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	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv471039	chr5:108133967-108245089	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1016343	chr5:108220116-108364687	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv882691	chr5:108229760-108366473	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108183800-108260400	Weak transcription	Ovary	ovary
2	chr5:108194600-108260000	Weak transcription	Fetal Intestine Large	intestine
3	chr5:108197000-108268200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr5:108199200-108271400	Weak transcription	Aorta	Aorta
5	chr5:108200200-108246400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:108203800-108323400	Weak transcription	Primary B cells from cord blood	blood
7	chr5:108208200-108268800	Weak transcription	Primary T cells from cord blood	blood
8	chr5:108214200-108272200	Weak transcription	Gastric	stomach
9	chr5:108217400-108244200	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr5:108217400-108253200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:108217600-108323200	Weak transcription	Left Ventricle	heart
12	chr5:108221400-108280600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:108223400-108247000	Weak transcription	Brain Substantia Nigra	brain
14	chr5:108227600-108244400	Weak transcription	Right Ventricle	heart
15	chr5:108227800-108245200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr5:108228600-108247600	Weak transcription	Liver	Liver
17	chr5:108229600-108244200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr5:108229600-108269800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:108230200-108302400	Weak transcription	HSMM	muscle
20	chr5:108230600-108249400	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:108230600-108260000	Weak transcription	Fetal Intestine Small	intestine
22	chr5:108234000-108246400	Weak transcription	Fetal Lung	lung
23	chr5:108235000-108253200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:108235200-108252400	Weak transcription	NHEK	skin
25	chr5:108235200-108253000	Weak transcription	Adipose Nuclei	Adipose
26	chr5:108235400-108246200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr5:108236600-108243400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:108236800-108253400	Weak transcription	NH-A	brain
29	chr5:108238200-108247400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr5:108240400-108252800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:108242200-108249400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:108242200-108271000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:108242600-108243000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:108242800-108252800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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