Variant report

Variant	rs883170
Chromosome Location	chr2:152830901-152830902
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	JUND	chr2:152830722-152830986	HepG2	liver:	n/a	chr2:152830857-152830866 chr2:152830858-152830865 chr2:152830855-152830867 chr2:152830857-152830865 chr2:152830855-152830866
2	FOS	chr2:152830696-152831003	MCF10A-Er-Src	breast:	n/a	chr2:152830857-152830866 chr2:152830858-152830865 chr2:152830855-152830867 chr2:152830857-152830865
3	MXI1	chr2:152829247-152830961	SK-N-SH	brain:	n/a	n/a
4	REST	chr2:152829432-152831044	H1-neurons	neurons:	n/a	n/a
5	RFX5	chr2:152829480-152831348	SK-N-SH	brain:	n/a	chr2:152830511-152830520
6	TEAD4	chr2:152829979-152830956	HepG2	liver:	n/a	chr2:152830666-152830675

Variant related genes	Relation type
CACNB4	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10930837	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs12463883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12475477	0.84[AMR][1000 genomes]
rs1356732	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs1474172	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1519710	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16830434	1.00[CEU][hapmap]
rs16830435	1.00[CEU][hapmap]
rs16830450	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs16830539	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3754532	1.00[CEU][hapmap]
rs4496331	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs4563220	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6730903	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs72621650	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7562260	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs7580901	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7581344	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7597915	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs867544	1.00[JPT][hapmap]
rs883157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952339	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv875290	chr2:152803129-152920126	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152827400-152834800	Weak transcription	Esophagus	oesophagus
2	chr2:152828800-152832800	Flanking Active TSS	HepG2	liver
3	chr2:152829000-152831000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:152829400-152831200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:152829800-152831000	Active TSS	Brain Anterior Caudate	brain
6	chr2:152829800-152831200	Enhancers	Fetal Thymus	thymus
7	chr2:152830000-152831000	Flanking Active TSS	Fetal Brain Male	brain
8	chr2:152830200-152831200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:152830200-152831600	Enhancers	Fetal Muscle Leg	muscle
10	chr2:152830200-152832000	Enhancers	Fetal Kidney	kidney
11	chr2:152830400-152831400	Enhancers	Fetal Muscle Trunk	muscle
12	chr2:152830400-152831800	Weak transcription	Fetal Intestine Large	intestine
13	chr2:152830600-152831200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:152830600-152831400	Enhancers	Fetal Lung	lung
15	chr2:152830600-152831600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:152830600-152832000	Weak transcription	Fetal Intestine Small	intestine
17	chr2:152830600-152833000	Weak transcription	GM12878-XiMat	blood
18	chr2:152830600-152833400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:152830600-152833400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:152830600-152836800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:152830600-152841200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:152830800-152831200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:152830800-152831200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:152830800-152831200	Enhancers	Brain Germinal Matrix	brain

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