Variant report

Variant	rs4577050
Chromosome Location	chr15:34528948-34528949
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	chr15:34516899..34518721-chr15:34526418..34530376,3	MCF-7	breast:
2	chr15:34526514..34531481-chr15:34531605..34533762,5	K562	blood:

Variant related genes	Relation type
ENSG00000140199	Chromatin interaction
ENSG00000128463	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10851952	0.80[JPT][hapmap]
rs10851964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11631981	0.81[ASN][1000 genomes]
rs12050753	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs12437551	0.80[JPT][hapmap]
rs12591315	0.81[ASN][1000 genomes]
rs16958878	0.80[ASN][1000 genomes]
rs17236763	0.81[ASN][1000 genomes]
rs17236777	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs17236784	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs17236798	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs17236819	0.83[ASN][1000 genomes]
rs17817800	0.87[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs17817806	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs2244040	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2290940	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs2290941	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs2290942	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs2705348	0.80[CEU][hapmap]
rs347848	0.81[CEU][hapmap]
rs347866	0.80[CEU][hapmap]
rs4530104	0.95[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4780231	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4780232	0.90[ASN][1000 genomes]
rs4780233	0.95[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4780234	0.89[ASN][1000 genomes]
rs56761496	0.80[ASN][1000 genomes]
rs57494441	0.81[ASN][1000 genomes]
rs59712831	0.81[ASN][1000 genomes]
rs60165224	0.83[ASN][1000 genomes]
rs60604568	0.83[ASN][1000 genomes]
rs61549125	0.80[ASN][1000 genomes]
rs6495639	0.84[ASN][1000 genomes]
rs6495646	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73388003	0.81[ASN][1000 genomes]
rs73388020	0.89[ASN][1000 genomes]
rs73388027	0.86[ASN][1000 genomes]
rs73388046	0.89[ASN][1000 genomes]
rs73388049	0.86[ASN][1000 genomes]
rs8035954	0.95[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8036468	0.80[JPT][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	nsv1052804	chr15:34498529-34841447	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv542341	chr15:34498529-34841447	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1045173	chr15:34501055-34596995	Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4577050	NOP10	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34517800-34531200	Weak transcription	Small Intestine	intestine
2	chr15:34518000-34532800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:34518000-34571800	Weak transcription	Stomach Mucosa	stomach
4	chr15:34518400-34531000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:34518800-34529000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:34518800-34548200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:34519000-34552400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr15:34519200-34530200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:34519200-34533200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr15:34519200-34534000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:34519200-34552200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:34519200-34553600	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr15:34519400-34530200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:34519400-34533200	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr15:34519400-34540800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:34519400-34552200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr15:34519400-34552200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:34519600-34531800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr15:34519600-34533400	Strong transcription	Duodenum Mucosa	Duodenum
20	chr15:34519600-34533400	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:34519600-34533600	Strong transcription	Fetal Muscle Trunk	muscle
22	chr15:34519600-34533600	Strong transcription	Fetal Muscle Leg	muscle
23	chr15:34519600-34538400	Strong transcription	Fetal Intestine Large	intestine
24	chr15:34519600-34544200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:34519600-34553600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr15:34519800-34531200	Strong transcription	GM12878-XiMat	blood
27	chr15:34519800-34533000	Strong transcription	Brain Anterior Caudate	brain
28	chr15:34519800-34540000	Strong transcription	Liver	Liver
29	chr15:34519800-34544800	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:34520000-34529600	Weak transcription	Fetal Heart	heart
31	chr15:34520000-34531400	Strong transcription	Fetal Brain Female	brain
32	chr15:34520200-34530200	Weak transcription	Psoas Muscle	Psoas
33	chr15:34520200-34555600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr15:34520800-34530800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr15:34521000-34532800	Weak transcription	K562	blood
36	chr15:34521000-34547800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:34521800-34531000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:34523000-34530400	Weak transcription	HMEC	breast
39	chr15:34523000-34532400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:34523000-34535800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:34523000-34545600	Weak transcription	Dnd41	blood
42	chr15:34523200-34530200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr15:34523200-34530200	Weak transcription	HUVEC	blood vessel
44	chr15:34523200-34530800	Weak transcription	NH-A	brain
45	chr15:34523200-34532600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:34523400-34530600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:34523800-34532400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:34524000-34529600	Strong transcription	Brain Germinal Matrix	brain
49	chr15:34524000-34530800	Strong transcription	HSMM	muscle
50	chr15:34524200-34533400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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