Variant report

Variant	rs11238472
Chromosome Location	chr10:43690253-43690254
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	chr10:43689923..43692438-chr10:43693060..43695471,2	MCF-7	breast:
2	chr10:43684501..43692416-chr10:43693896..43701465,17	K562	blood:

Variant related genes	Relation type
ENSG00000198915	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12244413	0.85[AMR][1000 genomes]
rs12570625	0.90[AMR][1000 genomes]
rs1800862	0.80[AMR][1000 genomes]
rs1955355	0.85[AMR][1000 genomes]
rs3026768	0.80[AMR][1000 genomes]
rs3026771	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3026775	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3026785	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs35718664	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs41298781	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs41301581	0.90[AMR][1000 genomes]
rs41301585	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv895082	chr10:43530071-43755506	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv895083	chr10:43549708-43765485	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1831010	chr10:43674916-43759185	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv895084	chr10:43688505-43765485	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11238472	GALNACT-2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43652600-43697200	Weak transcription	Pancreas	Pancrea
2	chr10:43658800-43690600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr10:43662200-43697600	Weak transcription	NHEK	skin
4	chr10:43667800-43692800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr10:43668200-43694000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:43672200-43690600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr10:43674000-43690600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr10:43674400-43697800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr10:43675600-43700600	Weak transcription	A549	lung
10	chr10:43675800-43697000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr10:43676600-43690600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr10:43677200-43692200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr10:43678800-43696800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr10:43679400-43690400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr10:43679400-43692000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr10:43679400-43692200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr10:43679400-43693400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr10:43679400-43694800	Weak transcription	Brain Substantia Nigra	brain
19	chr10:43679400-43697400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr10:43679600-43691800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:43679600-43693200	Weak transcription	Placenta	Placenta
22	chr10:43679800-43690400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr10:43680000-43691600	Weak transcription	Brain Angular Gyrus	brain
24	chr10:43680000-43697600	Weak transcription	NH-A	brain
25	chr10:43682000-43697400	Weak transcription	Liver	Liver
26	chr10:43682600-43690800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr10:43682600-43697400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr10:43682600-43697400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr10:43683000-43691800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr10:43683000-43693600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr10:43683000-43696000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr10:43683000-43697000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr10:43683000-43697200	Weak transcription	Primary B cells from cord blood	blood
34	chr10:43683000-43697400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr10:43683000-43697400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr10:43683000-43697400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr10:43683200-43690400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr10:43683200-43697000	Weak transcription	Fetal Brain Male	brain
39	chr10:43683200-43697200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr10:43683200-43697200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr10:43683400-43695200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr10:43683400-43697000	Weak transcription	Fetal Intestine Small	intestine
43	chr10:43683800-43692200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr10:43683800-43696600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr10:43683800-43697000	Weak transcription	Fetal Lung	lung
46	chr10:43684400-43690600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr10:43684400-43697200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr10:43684400-43697200	Weak transcription	Ovary	ovary
49	chr10:43684400-43697400	Weak transcription	Primary T cells from cord blood	blood
50	chr10:43684600-43690600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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