Variant report

Variant	rs10838684
Chromosome Location	chr11:47283862-47283863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47196892..47202921-chr11:47278417..47285951,9	MCF-7	breast:
2	chr11:47197941..47200223-chr11:47281634..47284173,2	K562	blood:
3	chr11:47279843..47284326-chr11:47288675..47293634,16	MCF-7	breast:
4	chr11:47183256..47186030-chr11:47281970..47284554,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110514	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000256746	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000149182	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10501321	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1052373	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1055510	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10742799	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10742801	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10769252	0.81[EUR][1000 genomes]
rs10838690	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10838691	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10838692	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10838693	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11039156	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11039166	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11039167	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12575456	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1375688	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1449627	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2013867	0.87[EUR][1000 genomes]
rs2167079	0.86[EUR][1000 genomes]
rs2279239	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2301216	0.83[AMR][1000 genomes]
rs326214	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs326222	0.87[EUR][1000 genomes]
rs35879051	0.90[EUR][1000 genomes]
rs3758669	0.87[EUR][1000 genomes]
rs3758672	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3758673	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3781621	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3781622	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3816725	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3847502	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4752822	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752824	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4752825	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4752980	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59663860	0.90[EUR][1000 genomes]
rs61896050	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6485746	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7109147	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7109203	0.84[EUR][1000 genomes]
rs7120118	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7120957	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7124955	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7127907	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7129661	0.88[EUR][1000 genomes]
rs7395581	0.85[EUR][1000 genomes]
rs7940809	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs830085	0.86[EUR][1000 genomes]
rs901746	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10838684	PACSIN3	cis	Esophagus Mucosa	GTEx
rs10838684	ACP2	cis	Thyroid	GTEx
rs10838684	ACP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47272400-47286400	Weak transcription	Dnd41	blood
2	chr11:47275800-47286800	Weak transcription	Primary T cells from cord blood	blood
3	chr11:47279200-47288800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:47279400-47286800	Weak transcription	NHEK	skin
5	chr11:47279400-47289400	Weak transcription	Fetal Brain Female	brain
6	chr11:47279800-47287000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:47279800-47289800	Weak transcription	Esophagus	oesophagus
8	chr11:47280000-47289400	Weak transcription	Brain Angular Gyrus	brain
9	chr11:47280000-47289600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:47280000-47290000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:47280200-47289400	Weak transcription	Pancreas	Pancrea
12	chr11:47280200-47289600	Weak transcription	Brain Substantia Nigra	brain
13	chr11:47280200-47289800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:47280200-47289800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:47280200-47290600	Weak transcription	Ovary	ovary
16	chr11:47280200-47290800	Weak transcription	Aorta	Aorta
17	chr11:47280600-47289800	Weak transcription	Fetal Kidney	kidney
18	chr11:47281000-47284800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr11:47281000-47285800	Weak transcription	Osteobl	bone
20	chr11:47281000-47286200	Weak transcription	NHDF-Ad	bronchial
21	chr11:47281000-47289800	Weak transcription	Fetal Brain Male	brain
22	chr11:47281000-47290800	Weak transcription	Small Intestine	intestine
23	chr11:47281200-47285800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:47281200-47285800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr11:47281200-47286200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr11:47281200-47286800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:47281200-47289000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:47281200-47289200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr11:47281200-47289400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:47281200-47289400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr11:47281200-47289400	Weak transcription	Fetal Lung	lung
32	chr11:47281200-47290000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:47281400-47284400	Weak transcription	K562	blood
34	chr11:47281400-47285800	Weak transcription	NHLF	lung
35	chr11:47281400-47288800	Weak transcription	Placenta	Placenta
36	chr11:47281400-47289400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr11:47281400-47289600	Weak transcription	Brain Hippocampus Middle	brain
38	chr11:47281600-47284800	Weak transcription	Fetal Thymus	thymus
39	chr11:47281600-47285600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr11:47281600-47286000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr11:47281600-47286200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr11:47281600-47286400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr11:47281600-47286400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr11:47281600-47286400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:47281600-47286800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr11:47281600-47286800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr11:47281600-47286800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr11:47281600-47286800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr11:47281600-47287000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr11:47281600-47287000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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