Variant report

Variant	rs10875713
Chromosome Location	chr12:48364463-48364464
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48363983..48366127-chr12:48370745..48372999,2	MCF-7	breast:
2	chr12:48362502..48365466-chr12:48366201..48368271,2	K562	blood:
3	chr12:48362584..48365917-chr12:48368904..48372045,3	K562	blood:
4	chr12:48356653..48359359-chr12:48363444..48365828,3	MCF-7	breast:
5	chr12:48356037..48360072-chr12:48360475..48364952,9	K562	blood:
6	chr12:48298891..48301417-chr12:48363482..48365531,2	K562	blood:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction
ENSG00000134291	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1015390	0.81[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs11168324	0.81[ASN][1000 genomes]
rs11534913	0.91[ASN][1000 genomes]
rs11541194	0.91[ASN][1000 genomes]
rs11561406	0.89[ASN][1000 genomes]
rs12721416	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12721420	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4073729	0.80[ASN][1000 genomes]
rs4494362	0.91[ASN][1000 genomes]
rs4760608	0.93[CEU][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes]
rs4760673	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv519174	chr12:48359984-48365265	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10875713	RP1-228P16.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48358200-48366200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:48358200-48366200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:48358400-48364600	Weak transcription	Ovary	ovary
4	chr12:48358400-48365000	Weak transcription	Osteobl	bone
5	chr12:48358400-48365200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:48358400-48366400	Weak transcription	Fetal Brain Male	brain
7	chr12:48358400-48367800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:48358400-48367800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:48358400-48369800	Weak transcription	Brain Angular Gyrus	brain
10	chr12:48358400-48373000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:48358600-48365200	Weak transcription	HSMMtube	muscle
12	chr12:48358600-48366600	Weak transcription	Fetal Lung	lung
13	chr12:48358600-48369400	Weak transcription	Fetal Kidney	kidney
14	chr12:48358600-48381400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:48358800-48366000	Weak transcription	HepG2	liver
16	chr12:48358800-48366200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:48359200-48364600	Strong transcription	Placenta	Placenta
18	chr12:48359200-48364800	Strong transcription	Primary T cells from cord blood	blood
19	chr12:48359200-48384000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:48359600-48366600	Strong transcription	Thymus	Thymus
21	chr12:48360000-48364600	Weak transcription	Right Ventricle	heart
22	chr12:48360000-48366000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:48360000-48368200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr12:48360200-48369600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr12:48360400-48364600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:48361000-48364600	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:48361200-48365000	Weak transcription	HUVEC	blood vessel
28	chr12:48361400-48364800	Weak transcription	Right Atrium	heart
29	chr12:48361800-48365000	Weak transcription	Brain Anterior Caudate	brain
30	chr12:48361800-48365000	Weak transcription	K562	blood
31	chr12:48361800-48366200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:48362200-48364600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:48362200-48364800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:48362200-48365200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr12:48362200-48366000	Weak transcription	Colonic Mucosa	Colon
36	chr12:48362200-48368000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr12:48362400-48370600	Weak transcription	HMEC	breast
38	chr12:48362400-48370800	Weak transcription	NHEK	skin
39	chr12:48362600-48364800	Weak transcription	GM12878-XiMat	blood
40	chr12:48362600-48365800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:48362600-48367200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:48362800-48366000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:48362800-48366200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr12:48362800-48367600	Weak transcription	Small Intestine	intestine
45	chr12:48362800-48368000	Weak transcription	Fetal Brain Female	brain
46	chr12:48363000-48364800	Weak transcription	A549	lung
47	chr12:48363000-48365200	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr12:48363000-48365200	Enhancers	Fetal Heart	heart
49	chr12:48363000-48365800	Weak transcription	Lung	lung
50	chr12:48363000-48367000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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