Variant report

Variant	rs11900816
Chromosome Location	chr2:86753805-86753806
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86751501..86754085-chr2:86847013..86850367,3	MCF-7	breast:
2	chr2:86752276..86754731-chr2:86755226..86757056,2	MCF-7	breast:
3	chr2:86752024..86755712-chr2:86758517..86761265,3	K562	blood:
4	chr2:86743323..86745032-chr2:86753355..86755938,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239305	Chromatin interaction
ENSG00000249884	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1036940	0.84[CEU][hapmap]
rs11127040	0.81[CEU][hapmap]
rs12995117	0.84[CEU][hapmap]
rs1468039	0.82[CEU][hapmap]
rs1518811	0.82[CEU][hapmap]
rs2044230	0.84[CEU][hapmap]
rs4832290	0.84[CEU][hapmap]
rs4832294	0.84[CEU][hapmap]
rs6714826	0.84[CEU][hapmap]
rs950780	0.82[CEU][hapmap]

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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11900816	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:86728200-86755800	Weak transcription	Fetal Brain Male	brain
3	chr2:86733000-86759400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:86733400-86758600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:86734000-86784800	Weak transcription	Osteobl	bone
6	chr2:86736400-86770600	Weak transcription	Brain Angular Gyrus	brain
7	chr2:86736800-86754400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:86737000-86754400	Weak transcription	NHDF-Ad	bronchial
9	chr2:86737000-86761200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:86737000-86772800	Weak transcription	Pancreas	Pancrea
11	chr2:86737400-86755400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:86737400-86756800	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:86737400-86757400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:86737400-86788400	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:86737600-86768400	Weak transcription	Ovary	ovary
16	chr2:86737800-86754400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:86737800-86755400	Weak transcription	Small Intestine	intestine
18	chr2:86737800-86756400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:86737800-86779600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:86738200-86756200	Weak transcription	Brain Substantia Nigra	brain
21	chr2:86738200-86772400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:86738200-86772600	Weak transcription	Right Ventricle	heart
23	chr2:86738400-86759000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr2:86741400-86754200	Weak transcription	Left Ventricle	heart
25	chr2:86741400-86768400	Weak transcription	Psoas Muscle	Psoas
26	chr2:86742400-86755600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:86744000-86755600	Weak transcription	Fetal Brain Female	brain
28	chr2:86746000-86754400	Weak transcription	HSMMtube	muscle
29	chr2:86746000-86768000	Weak transcription	Fetal Heart	heart
30	chr2:86747600-86754800	Weak transcription	Esophagus	oesophagus
31	chr2:86747800-86755000	Weak transcription	Brain Anterior Caudate	brain
32	chr2:86748000-86754000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:86748000-86754400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:86748000-86754600	Weak transcription	Thymus	Thymus
35	chr2:86748000-86754600	Weak transcription	A549	lung
36	chr2:86748000-86755200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:86748000-86755200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:86748000-86755200	Weak transcription	HUVEC	blood vessel
39	chr2:86748000-86755800	Weak transcription	Spleen	Spleen
40	chr2:86748000-86756400	Weak transcription	Fetal Lung	lung
41	chr2:86748000-86757000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr2:86748000-86758000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:86748000-86758000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr2:86748000-86758600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:86748000-86760600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:86748000-86770600	Weak transcription	Gastric	stomach
47	chr2:86748200-86759000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr2:86749000-86755200	Weak transcription	GM12878-XiMat	blood
49	chr2:86749000-86755800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:86749200-86756600	Strong transcription	Primary B cells from cord blood	blood

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