Variant report

Variant	rs2305573
Chromosome Location	chr2:33747285-33747286
allele	C/T
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	NFIC	chr2:33746589-33747551	SK-N-SH	brain:	n/a	chr2:33746923-33746939 chr2:33746922-33746939
2	TCF12	chr2:33746610-33747523	SK-N-SH	brain:	n/a	n/a
3	EP300	chr2:33746690-33747427	SK-N-SH_RA	brain:	n/a	n/a
4	REST	chr2:33746906-33748309	H1-neurons	neurons:	n/a	n/a
5	EP300	chr2:33746699-33747331	SK-N-SH_RA	brain:	n/a	n/a
6	PBX3	chr2:33746721-33747513	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr2:33746674-33747512	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr2:33744673-33747922	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:33744652-33747909	GM12891	blood:	n/a	n/a
10	TCF12	chr2:33746680-33747581	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr2:33746650-33747586	SK-N-SH	brain:	n/a	n/a
12	JUND	chr2:33746701-33747374	SK-N-SH	brain:	n/a	n/a
13	GATA3	chr2:33746660-33747561	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:33736575..33738622-chr2:33744601..33747381,2	K562	blood:

Variant related genes	Relation type
RASGRP3	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10200743	0.82[CHB][hapmap];0.97[GIH][hapmap];0.84[TSI][hapmap]
rs2124439	0.86[CEU][hapmap];0.94[CHB][hapmap];0.86[EUR][1000 genomes]
rs4286255	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4355083	0.83[EUR][1000 genomes]
rs4561642	0.91[CEU][hapmap];0.89[CHB][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs4670648	0.86[CEU][hapmap];0.88[CHB][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs4670659	0.95[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4670683	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6729768	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6729792	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7565568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7581376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2305573	CEBPZ	cis	parietal	SCAN
rs2305573	RASGRP3	cis	lymphoblastoid	seeQTL
rs2305573	ADPRHL2	trans	parietal	SCAN
rs2305573	SLC30A6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33710400-33775400	Weak transcription	Pancreas	Pancrea
2	chr2:33712200-33747600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:33728800-33750800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:33730000-33751600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:33735400-33761800	Weak transcription	Spleen	Spleen
6	chr2:33735800-33754800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:33737400-33749800	Strong transcription	GM12878-XiMat	blood
8	chr2:33737600-33760800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:33738600-33782800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:33738800-33777200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:33739200-33761800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:33740000-33752000	Weak transcription	Lung	lung
13	chr2:33740800-33751200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:33740800-33754600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:33740800-33790000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr2:33744600-33747400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:33744800-33758200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:33745400-33750800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr2:33745400-33753400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:33745800-33748200	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:33746000-33747400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:33746000-33747400	Enhancers	Aorta	Aorta
23	chr2:33746200-33748000	Enhancers	Fetal Stomach	stomach
24	chr2:33746200-33748400	Enhancers	Fetal Heart	heart
25	chr2:33746400-33747600	Weak transcription	Left Ventricle	heart
26	chr2:33746400-33748000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:33746400-33748200	Enhancers	NHDF-Ad	bronchial
28	chr2:33746400-33749000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:33746600-33747400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:33746600-33747400	Enhancers	Adipose Nuclei	Adipose
31	chr2:33746600-33748000	Enhancers	Brain Hippocampus Middle	brain
32	chr2:33746600-33748000	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr2:33746600-33748000	Enhancers	Brain Substantia Nigra	brain
34	chr2:33746600-33748200	Enhancers	Brain Angular Gyrus	brain
35	chr2:33746800-33747600	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr2:33746800-33747800	Enhancers	Brain Anterior Caudate	brain
37	chr2:33746800-33747800	Enhancers	Colon Smooth Muscle	Colon
38	chr2:33746800-33747800	Enhancers	Right Ventricle	heart
39	chr2:33746800-33747800	Enhancers	Osteobl	bone
40	chr2:33746800-33748000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:33746800-33748000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr2:33746800-33748000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:33746800-33748000	Enhancers	Brain Cingulate Gyrus	brain
44	chr2:33746800-33748000	Enhancers	Rectal Smooth Muscle	rectum
45	chr2:33747000-33747800	Enhancers	Ovary	ovary
46	chr2:33747000-33748000	Enhancers	Stomach Smooth Muscle	stomach
47	chr2:33747200-33747600	Weak transcription	Fetal Kidney	kidney
48	chr2:33747200-33751200	Weak transcription	Primary B cells from cord blood	blood
49	chr2:33747200-33755000	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:33747200-33757600	Weak transcription	Psoas Muscle	Psoas

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