Variant report

Variant	rs2293254
Chromosome Location	chr2:36740643-36740644
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:36740613-36741022	A549	lung:	n/a	n/a
2	POLR2A	chr2:36740447-36741327	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr2:36740108-36741806	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr2:36740537-36740989	ProgFib	skin:	n/a	n/a
5	POLR2A	chr2:36740548-36741075	A549	lung:	n/a	n/a

Variant related genes	Relation type
CRIM1	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10184223	0.96[CEU][hapmap];0.89[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11681392	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs11694761	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1523785	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs2287082	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3755197	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs3770821	0.83[CEU][hapmap]
rs3770822	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs3770832	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3770833	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3815552	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs848522	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs848523	0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs848525	0.81[ASN][1000 genomes]
rs848564	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs861050	0.86[CEU][hapmap]

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	nsv833803	chr2:36589065-36745779	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	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
3	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2293254	FEZ2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36705000-36743200	Weak transcription	Brain Germinal Matrix	brain
2	chr2:36710000-36743400	Weak transcription	Primary T cells from cord blood	blood
3	chr2:36713800-36789600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:36717400-36744400	Weak transcription	Brain Angular Gyrus	brain
5	chr2:36720000-36760600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:36721800-36746000	Strong transcription	HUVEC	blood vessel
7	chr2:36722600-36752400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:36725200-36756800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:36726800-36751800	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:36727400-36757200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:36727600-36740800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:36727600-36743600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:36728400-36749200	Weak transcription	Fetal Brain Male	brain
14	chr2:36729600-36790200	Weak transcription	Small Intestine	intestine
15	chr2:36733000-36752000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:36733200-36743400	Strong transcription	NHEK	skin
17	chr2:36733200-36774200	Weak transcription	Fetal Thymus	thymus
18	chr2:36733400-36764400	Weak transcription	Pancreas	Pancrea
19	chr2:36733600-36748800	Weak transcription	Stomach Mucosa	stomach
20	chr2:36733600-36750200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr2:36734600-36756800	Strong transcription	HepG2	liver
22	chr2:36735400-36744200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:36735600-36754200	Strong transcription	Hela-S3	cervix
24	chr2:36735800-36751000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:36735800-36752600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:36736000-36745000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:36736000-36755800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:36736400-36741000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:36736400-36751400	Strong transcription	Left Ventricle	heart
30	chr2:36736800-36751400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:36737200-36745200	Strong transcription	Fetal Stomach	stomach
32	chr2:36737600-36742600	Strong transcription	Primary hematopoietic stem cells	blood
33	chr2:36737800-36748600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr2:36737800-36750600	Strong transcription	A549	lung
35	chr2:36738000-36744600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:36738000-36745000	Genic enhancers	Placenta	Placenta
37	chr2:36738000-36747200	Weak transcription	Thymus	Thymus
38	chr2:36738200-36745000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:36738200-36745200	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:36738200-36754000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr2:36738400-36745200	Strong transcription	Aorta	Aorta
42	chr2:36738400-36751600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:36738400-36751600	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:36738600-36754200	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:36738800-36740800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:36738800-36741400	Strong transcription	Rectal Smooth Muscle	rectum
47	chr2:36738800-36743200	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr2:36738800-36743400	Strong transcription	HMEC	breast
49	chr2:36738800-36745000	Strong transcription	Lung	lung
50	chr2:36738800-36748200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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