Variant report

Variant	rs7565568
Chromosome Location	chr2:33746806-33746807
allele	A/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	POLR2A	chr2:33746750-33747106	SK-N-SH	brain:	n/a	n/a
2	NFIC	chr2:33746589-33747551	SK-N-SH	brain:	n/a	chr2:33746923-33746939 chr2:33746922-33746939
3	TCF12	chr2:33746610-33747523	SK-N-SH	brain:	n/a	n/a
4	EP300	chr2:33746690-33747427	SK-N-SH_RA	brain:	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	STAT3	chr2:33746754-33746918	MCF10A-Er-Src	breast:	n/a	n/a
8	PBX3	chr2:33746674-33747512	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr2:33744673-33747922	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:33744652-33747909	GM12891	blood:	n/a	n/a
11	TCF12	chr2:33746680-33747581	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr2:33746650-33747586	SK-N-SH	brain:	n/a	n/a
13	JUND	chr2:33746701-33747374	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr2:33746660-33747561	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:33702588..33705548-chr2:33744716..33747266,2	K562	blood:
2	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:10)

rs_ID	r²[population]
rs10200743	0.82[CHB][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap]
rs2124439	0.86[CEU][hapmap];0.94[CHB][hapmap]
rs2305573	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]
rs4286255	0.81[EUR][1000 genomes]
rs4561642	0.91[CEU][hapmap];0.89[CHB][hapmap];0.92[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs4670648	0.86[CEU][hapmap];0.88[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs4670659	0.95[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4670683	0.85[AMR][1000 genomes]
rs6729768	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7581376	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7565568	ADPRHL2	trans	parietal	SCAN
rs7565568	CEBPZ	cis	parietal	SCAN
rs7565568	SLC30A6	cis	parietal	SCAN
rs7565568	RASGRP3	cis	lymphoblastoid	seeQTL

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	chr2:33739200-33747000	Weak transcription	Fetal Kidney	kidney
12	chr2:33739200-33761800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:33740000-33752000	Weak transcription	Lung	lung
14	chr2:33740800-33751200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:33740800-33754600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:33740800-33790000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr2:33744600-33747200	Strong transcription	Primary B cells from cord blood	blood
18	chr2:33744600-33747400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:33744800-33758200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:33745400-33750800	Strong transcription	Primary B cells from peripheral blood	blood
21	chr2:33745400-33753400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:33745800-33748200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:33746000-33747400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:33746000-33747400	Enhancers	Aorta	Aorta
25	chr2:33746200-33747200	Enhancers	Fetal Muscle Leg	muscle
26	chr2:33746200-33748000	Enhancers	Fetal Stomach	stomach
27	chr2:33746200-33748400	Enhancers	Fetal Heart	heart
28	chr2:33746400-33747600	Weak transcription	Left Ventricle	heart
29	chr2:33746400-33748000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:33746400-33748200	Enhancers	NHDF-Ad	bronchial
31	chr2:33746400-33749000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:33746600-33747400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:33746600-33747400	Enhancers	Adipose Nuclei	Adipose
34	chr2:33746600-33748000	Enhancers	Brain Hippocampus Middle	brain
35	chr2:33746600-33748000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr2:33746600-33748000	Enhancers	Brain Substantia Nigra	brain
37	chr2:33746600-33748200	Enhancers	Brain Angular Gyrus	brain
38	chr2:33746800-33747000	Enhancers	Fetal Lung	lung
39	chr2:33746800-33747000	Enhancers	Right Atrium	heart
40	chr2:33746800-33747200	Enhancers	Psoas Muscle	Psoas
41	chr2:33746800-33747600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr2:33746800-33747800	Enhancers	Brain Anterior Caudate	brain
43	chr2:33746800-33747800	Enhancers	Colon Smooth Muscle	Colon
44	chr2:33746800-33747800	Enhancers	Right Ventricle	heart
45	chr2:33746800-33747800	Enhancers	Osteobl	bone
46	chr2:33746800-33748000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:33746800-33748000	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr2:33746800-33748000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:33746800-33748000	Enhancers	Brain Cingulate Gyrus	brain
50	chr2:33746800-33748000	Enhancers	Rectal Smooth Muscle	rectum

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