Variant report

Variant	rs4275539
Chromosome Location	chr10:200144-200145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:179114..184532-chr10:197541..200873,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000015171	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10508201	0.81[CEU][hapmap]
rs10736951	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs10794721	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11250292	0.81[EUR][1000 genomes]
rs11250419	0.82[EUR][1000 genomes]
rs11250488	0.89[EUR][1000 genomes]
rs11250528	0.89[EUR][1000 genomes]
rs11250529	0.86[EUR][1000 genomes]
rs11250575	0.84[EUR][1000 genomes]
rs11250790	0.90[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs11250797	0.82[JPT][hapmap]
rs11592007	0.81[EUR][1000 genomes]
rs11592027	0.81[EUR][1000 genomes]
rs11594308	0.82[EUR][1000 genomes]
rs1367896	0.94[YRI][hapmap];0.80[AFR][1000 genomes]
rs1476129	1.00[YRI][hapmap]
rs1476130	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17221197	0.84[EUR][1000 genomes]
rs17221225	0.81[CEU][hapmap]
rs17221239	0.91[CEU][hapmap]
rs2303990	0.82[YRI][hapmap]
rs2379049	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2436024	1.00[YRI][hapmap]
rs2436025	0.94[YRI][hapmap]
rs2436030	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2448364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2448365	1.00[YRI][hapmap]
rs2448366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2448369	1.00[YRI][hapmap]
rs2448371	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2448373	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2448374	1.00[YRI][hapmap]
rs2448377	1.00[YRI][hapmap]
rs2448380	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2448381	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2448382	1.00[YRI][hapmap]
rs2448384	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2496274	0.93[YRI][hapmap]
rs2496275	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2496277	1.00[YRI][hapmap]
rs2496278	0.91[CEU][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2496279	1.00[YRI][hapmap]
rs3123252	0.94[YRI][hapmap]
rs3131995	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3132006	0.88[YRI][hapmap]
rs34926441	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3740303	0.88[YRI][hapmap]
rs4331015	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4369322	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4390277	0.80[AFR][1000 genomes]
rs4504990	0.81[AFR][1000 genomes]
rs4537685	0.80[AFR][1000 genomes]
rs4600135	0.94[YRI][hapmap]
rs4880809	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs56217646	0.81[EUR][1000 genomes]
rs61836334	0.81[EUR][1000 genomes]
rs61836335	0.81[EUR][1000 genomes]
rs6560723	0.80[AFR][1000 genomes]
rs7089302	0.81[EUR][1000 genomes]
rs7089889	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7090608	0.83[EUR][1000 genomes]
rs7476951	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7896421	0.82[CEU][hapmap]
rs7898275	0.81[AFR][1000 genomes]
rs7905732	1.00[YRI][hapmap]
rs7909028	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7909116	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7912326	0.82[CEU][hapmap]
rs7918734	0.81[AFR][1000 genomes]
rs7919162	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7919436	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7919991	0.81[AFR][1000 genomes]
rs9329277	0.83[AFR][1000 genomes]
rs9419432	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9419493	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9419496	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531919	chr10:60001-668649	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1040332	chr10:72797-244561	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1044775	chr10:72797-250662	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats 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	11 gene(s)	inside rSNPs	diseases
4	nsv1047868	chr10:72797-259003	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1048232	chr10:72797-274675	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:183200-205400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr10:183400-200800	Weak transcription	Thymus	Thymus
3	chr10:184400-200200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr10:188000-200400	Weak transcription	Primary B cells from cord blood	blood
5	chr10:188800-202600	Weak transcription	A549	lung
6	chr10:189000-204000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr10:189000-208800	Weak transcription	Small Intestine	intestine
8	chr10:189200-201800	Weak transcription	Brain Hippocampus Middle	brain
9	chr10:189400-200200	Weak transcription	Fetal Heart	heart
10	chr10:190400-200200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr10:190400-215200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr10:190600-203200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:190600-212800	Weak transcription	Left Ventricle	heart
14	chr10:194000-211400	Weak transcription	Fetal Lung	lung
15	chr10:194200-228200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr10:194600-210400	Weak transcription	Primary T cells from cord blood	blood
17	chr10:194800-200200	Weak transcription	Gastric	stomach
18	chr10:194800-206200	Weak transcription	Pancreas	Pancrea
19	chr10:194800-212600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr10:195400-207000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr10:196400-206200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr10:196800-215000	Weak transcription	Fetal Intestine Large	intestine
23	chr10:197000-200800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr10:197000-209600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr10:197200-200200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr10:197400-209200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr10:197400-210400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr10:197400-211200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr10:197800-219800	Weak transcription	HUVEC	blood vessel
30	chr10:198400-200200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr10:198600-206000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr10:199000-200400	Enhancers	HSMM	muscle
33	chr10:199600-200400	Enhancers	Adipose Nuclei	Adipose
34	chr10:199600-200400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr10:199600-200400	Enhancers	Spleen	Spleen
36	chr10:199600-200600	Enhancers	Ovary	ovary
37	chr10:199600-209800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr10:199800-200200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr10:199800-200400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr10:199800-200400	Enhancers	Psoas Muscle	Psoas
41	chr10:199800-200400	Enhancers	Right Ventricle	heart
42	chr10:199800-200400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr10:199800-200400	Enhancers	HSMMtube	muscle
44	chr10:199800-200400	Enhancers	Osteobl	bone
45	chr10:199800-200600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr10:199800-200600	Enhancers	NH-A	brain
47	chr10:200000-200400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr10:200000-200400	Enhancers	NHDF-Ad	bronchial
49	chr10:200000-200400	Enhancers	NHLF	lung
50	chr10:200000-200600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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