Variant report

Variant	rs13105599
Chromosome Location	chr4:158937609-158937610
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:158934945..158937629-chr4:158953752..158956012,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10018872	1.00[CEU][hapmap]
rs10022190	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10024133	1.00[CEU][hapmap]
rs10517689	1.00[CEU][hapmap]
rs11100151	1.00[CEU][hapmap]
rs11731973	1.00[JPT][hapmap]
rs11938464	1.00[CEU][hapmap]
rs12502811	1.00[CEU][hapmap]
rs12511679	1.00[CEU][hapmap]
rs12511713	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13101806	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13105388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13119344	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13123367	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13128845	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13149552	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320370	1.00[CEU][hapmap]
rs1320371	1.00[CEU][hapmap]
rs17036867	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17036927	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346320	1.00[CEU][hapmap]
rs2346381	1.00[CEU][hapmap]
rs2346776	1.00[CEU][hapmap]
rs2346780	1.00[CEU][hapmap]
rs2346783	1.00[CEU][hapmap]
rs28717075	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34009182	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34030902	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34131483	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34387852	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34535065	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34735033	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34765608	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35346320	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35439222	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35465944	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35473373	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35518318	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36069561	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4389619	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4391084	1.00[CEU][hapmap]
rs4472184	1.00[CEU][hapmap]
rs4569796	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4582199	1.00[CEU][hapmap]
rs4690893	1.00[CEU][hapmap]
rs4691456	1.00[CEU][hapmap]
rs4691457	1.00[CEU][hapmap]
rs4691458	0.82[CEU][hapmap]
rs4691462	1.00[CEU][hapmap]
rs4691463	1.00[CEU][hapmap]
rs4691465	1.00[CEU][hapmap]
rs4691467	1.00[CEU][hapmap]
rs5004547	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6536292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6812635	1.00[CEU][hapmap]
rs6821598	1.00[CEU][hapmap]
rs6832099	1.00[CEU][hapmap]
rs6846661	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6849902	1.00[CEU][hapmap]
rs6852646	1.00[CEU][hapmap]
rs6855420	1.00[CEU][hapmap]
rs71607171	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7437833	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664258	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664738	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665295	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671094	1.00[CEU][hapmap]
rs7671501	1.00[CEU][hapmap]
rs7671934	1.00[CEU][hapmap]
rs7687980	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7691126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695599	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv881288	chr4:158891733-159028080	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:158923800-158939400	Weak transcription	HepG2	liver
2	chr4:158926000-158938800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:158930200-158940800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:158930400-158940800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:158930600-158940800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:158930800-158941400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:158932600-158941400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:158933000-158938600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr4:158933000-158938800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:158934200-158941400	Enhancers	HUVEC	blood vessel
11	chr4:158934400-158938200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:158934600-158938200	Enhancers	HSMM	muscle
13	chr4:158934600-158943800	Enhancers	NHDF-Ad	bronchial
14	chr4:158934800-158939200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr4:158935600-158939400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:158935800-158938200	Enhancers	HMEC	breast
17	chr4:158935800-158938400	Enhancers	Osteobl	bone
18	chr4:158936000-158941600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:158936200-158939600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:158936200-158942600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:158936400-158938200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:158936600-158938800	Weak transcription	NHLF	lung
23	chr4:158936600-158941200	Weak transcription	NHEK	skin
24	chr4:158936800-158938200	Enhancers	NH-A	brain
25	chr4:158936800-158939200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:158936800-158939400	Weak transcription	HSMMtube	muscle
27	chr4:158936800-158939600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr4:158936800-158940800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr4:158936800-158941400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:158937200-158938600	Weak transcription	Ovary	ovary
31	chr4:158937200-158939600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:158937200-158947000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:158937200-158947200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:158937400-158938000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:158937400-158938000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr4:158937600-158938000	Enhancers	Brain Substantia Nigra	brain
37	chr4:158937600-158938200	Enhancers	A549	lung
38	chr4:158937600-158939200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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