Variant report

Variant	rs3821153
Chromosome Location	chr2:36753122-36753123
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2023409	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3770826	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3821156	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848522	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs848523	0.96[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs848525	0.81[EUR][1000 genomes]
rs848564	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs861050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs884215	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][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	nsv1010985	chr2:36707157-36942066	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv535642	chr2:36707157-36942066	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3821153	FEZ2	cis	cerebellum	SCAN
rs3821153	CDC42EP3	cis	parietal	SCAN
rs3821153	CDC42EP3	cis	cerebellum	SCAN
rs3821153	CRIM1	cis	cerebellum	SCAN
rs3821153	FEZ2	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36713800-36789600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:36720000-36760600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:36725200-36756800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:36727400-36757200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:36729600-36790200	Weak transcription	Small Intestine	intestine
6	chr2:36733200-36774200	Weak transcription	Fetal Thymus	thymus
7	chr2:36733400-36764400	Weak transcription	Pancreas	Pancrea
8	chr2:36734600-36756800	Strong transcription	HepG2	liver
9	chr2:36735600-36754200	Strong transcription	Hela-S3	cervix
10	chr2:36736000-36755800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:36738200-36754000	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr2:36738600-36754200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:36738800-36754000	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr2:36739000-36778200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:36739400-36757400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:36740200-36754000	Strong transcription	Adipose Nuclei	Adipose
17	chr2:36740200-36754800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr2:36744000-36754200	Strong transcription	Primary hematopoietic stem cells	blood
19	chr2:36744000-36754400	Strong transcription	HMEC	breast
20	chr2:36744000-36755600	Strong transcription	NH-A	brain
21	chr2:36744000-36756600	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr2:36744200-36756600	Strong transcription	HSMM	muscle
23	chr2:36744800-36754200	Strong transcription	HSMMtube	muscle
24	chr2:36744800-36764200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:36745000-36755600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:36745000-36756800	Strong transcription	Placenta	Placenta
27	chr2:36745000-36757800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:36747800-36766200	Weak transcription	Thymus	Thymus
29	chr2:36747800-36768800	Weak transcription	Colonic Mucosa	Colon
30	chr2:36747800-36774200	Weak transcription	Liver	Liver
31	chr2:36748000-36757400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:36748000-36757400	Weak transcription	Brain Substantia Nigra	brain
33	chr2:36748000-36764400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:36748000-36764400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:36748200-36757400	Weak transcription	Fetal Heart	heart
36	chr2:36749000-36754000	Strong transcription	Fetal Intestine Large	intestine
37	chr2:36749200-36758000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr2:36749600-36756600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:36749600-36764200	Weak transcription	Brain Germinal Matrix	brain
40	chr2:36749600-36765000	Weak transcription	Fetal Brain Male	brain
41	chr2:36749600-36765200	Weak transcription	Right Ventricle	heart
42	chr2:36749800-36764200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:36749800-36764200	Weak transcription	Spleen	Spleen
44	chr2:36750000-36765200	Weak transcription	Gastric	stomach
45	chr2:36750200-36754200	Strong transcription	Primary B cells from cord blood	blood
46	chr2:36750600-36757000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:36750800-36756400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:36750800-36757200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:36750800-36757200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:36750800-36759000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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