Variant report

Variant	rs4664512
Chromosome Location	chr2:152829557-152829558
allele	A/C/G/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	MXI1	chr2:152829247-152830961	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr2:152829421-152830780	H1-neurons	neurons:	n/a	n/a
3	REST	chr2:152829432-152831044	H1-neurons	neurons:	n/a	n/a
4	RFX5	chr2:152829480-152831348	SK-N-SH	brain:	n/a	chr2:152830511-152830520

Variant related genes	Relation type
CACNB4	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10178110	1.00[JPT][hapmap]
rs10184416	1.00[JPT][hapmap]
rs10200299	0.83[AMR][1000 genomes]
rs10497090	1.00[JPT][hapmap]
rs10497091	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs10930839	1.00[JPT][hapmap]
rs11895837	1.00[JPT][hapmap]
rs12472173	0.84[CEU][hapmap]
rs12693174	0.82[EUR][1000 genomes]
rs12992504	0.84[CEU][hapmap]
rs13000853	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs13391908	0.83[AMR][1000 genomes]
rs13394320	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs13413766	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13421962	1.00[JPT][hapmap]
rs13432920	0.83[AMR][1000 genomes]
rs1519713	0.84[CEU][hapmap]
rs1519714	1.00[JPT][hapmap]
rs1554365	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17270290	1.00[JPT][hapmap]
rs17270332	0.85[CEU][hapmap]
rs17270346	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1963671	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs2010310	0.80[CEU][hapmap];0.86[CHB][hapmap]
rs34880899	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4664070	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4664073	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4664510	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664521	0.84[CEU][hapmap]
rs6433733	0.85[CEU][hapmap]
rs6725537	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6727592	0.85[CEU][hapmap]
rs6742375	1.00[JPT][hapmap]
rs6751763	0.85[CEU][hapmap]
rs6756595	0.82[CEU][hapmap]
rs6756645	1.00[JPT][hapmap]
rs71350311	0.83[AMR][1000 genomes]
rs7558481	0.85[CEU][hapmap]
rs7591461	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7602165	0.84[CEU][hapmap]
rs867437	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs908937	1.00[JPT][hapmap]

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:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152824800-152830200	Weak transcription	Right Atrium	heart
2	chr2:152827400-152834800	Weak transcription	Esophagus	oesophagus
3	chr2:152827800-152830800	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr2:152828200-152829600	Enhancers	Fetal Lung	lung
5	chr2:152828200-152829800	Flanking Active TSS	Brain Anterior Caudate	brain
6	chr2:152828400-152830200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:152828600-152829600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:152828600-152829800	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr2:152828800-152829600	Flanking Active TSS	Fetal Brain Male	brain
10	chr2:152828800-152830000	Flanking Active TSS	Brain Cingulate Gyrus	brain
11	chr2:152828800-152830200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:152828800-152832800	Flanking Active TSS	HepG2	liver
13	chr2:152829000-152829600	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr2:152829000-152829800	Flanking Active TSS	Brain Substantia Nigra	brain
15	chr2:152829000-152830600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr2:152829000-152830800	Active TSS	Brain Germinal Matrix	brain
17	chr2:152829000-152831000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:152829200-152829600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:152829200-152830200	Weak transcription	GM12878-XiMat	blood
20	chr2:152829200-152830800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr2:152829200-152830800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:152829400-152829600	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr2:152829400-152829600	Active TSS	Fetal Brain Female	brain
24	chr2:152829400-152829800	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr2:152829400-152829800	Flanking Active TSS	Brain Angular Gyrus	brain
26	chr2:152829400-152830000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:152829400-152830200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:152829400-152830400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr2:152829400-152830400	Active TSS	Fetal Intestine Large	intestine
30	chr2:152829400-152830600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr2:152829400-152830600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr2:152829400-152831200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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