Variant report

Variant	rs10900727
Chromosome Location	chr5:118412344-118412345
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118405957..118409296-chr5:118409304..118413767,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172869	Chromatin interaction
ENSG00000249494	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10052879	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs10064311	1.00[JPT][hapmap]
rs10071407	1.00[JPT][hapmap]
rs12653870	1.00[CHD][hapmap]
rs1394629	1.00[JPT][hapmap]
rs299192	1.00[JPT][hapmap]
rs4286709	1.00[JPT][hapmap]
rs4380699	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4512152	0.91[ASN][1000 genomes]
rs4583917	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4895185	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs62374136	0.82[ASN][1000 genomes]
rs6595174	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs6595178	1.00[JPT][hapmap]
rs6863826	1.00[CHD][hapmap]
rs6880622	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs6889308	1.00[JPT][hapmap]
rs6893733	1.00[JPT][hapmap]
rs6894997	1.00[JPT][hapmap]
rs7702867	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7720231	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs7734532	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7736400	1.00[JPT][hapmap]
rs9327087	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9327093	1.00[JPT][hapmap]
rs9790885	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015878	chr5:118288904-118414706	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537881	chr5:118288904-118414706	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv882774	chr5:118325429-118553470	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1018539	chr5:118355284-118445244	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription 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
5	esv3511406	chr5:118409810-118459495	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3511407	chr5:118409863-118459482	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118407600-118413000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr5:118407600-118423600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:118407800-118412400	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr5:118407800-118413800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:118407800-118421600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr5:118407800-118456600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:118408000-118414600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:118408000-118414600	Weak transcription	HSMM	muscle
9	chr5:118408400-118451800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:118408600-118414400	Weak transcription	Osteobl	bone
11	chr5:118408600-118414600	Weak transcription	Fetal Intestine Small	intestine
12	chr5:118408600-118414800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:118408800-118414600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:118408800-118414800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:118409000-118412800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr5:118409000-118413200	Weak transcription	Fetal Brain Male	brain
17	chr5:118409000-118414200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:118409000-118414200	Weak transcription	Right Ventricle	heart
19	chr5:118409000-118414400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:118409000-118414400	Weak transcription	NHEK	skin
21	chr5:118409000-118414800	Weak transcription	Right Atrium	heart
22	chr5:118409000-118415600	Weak transcription	Left Ventricle	heart
23	chr5:118409000-118415800	Weak transcription	Fetal Muscle Leg	muscle
24	chr5:118409000-118420400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr5:118409000-118424000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr5:118409000-118435000	Weak transcription	Lung	lung
27	chr5:118409000-118471200	Weak transcription	Gastric	stomach
28	chr5:118409200-118414200	Weak transcription	Psoas Muscle	Psoas
29	chr5:118409200-118414400	Weak transcription	Fetal Thymus	thymus
30	chr5:118409200-118414600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:118409200-118414600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:118409200-118414600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:118409200-118414600	Weak transcription	Fetal Lung	lung
34	chr5:118409200-118415000	Weak transcription	NHDF-Ad	bronchial
35	chr5:118409200-118416000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr5:118409200-118416600	Weak transcription	Brain Angular Gyrus	brain
37	chr5:118409200-118416600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:118409200-118418000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:118409200-118419400	Weak transcription	Fetal Stomach	stomach
40	chr5:118409200-118424000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr5:118409400-118414200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:118409400-118414200	Weak transcription	Small Intestine	intestine
43	chr5:118409400-118414200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr5:118409400-118414200	Weak transcription	Thymus	Thymus
45	chr5:118409400-118414400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:118409400-118414400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:118409400-118414600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:118409400-118414800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr5:118409400-118421000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr5:118409400-118435000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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