Variant report

Variant	rs11892564
Chromosome Location	chr2:213226544-213226545
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:213217638..213221383-chr2:213223310..213226579,3	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10174236	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497972	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13383860	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs13383978	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13384603	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13395813	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1394799	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16848525	1.00[CHB][hapmap]
rs28623294	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62184101	0.95[ASN][1000 genomes]
rs6435700	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006051	chr2:213052804-213273642	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv584346	chr2:213067749-213258622	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv834526	chr2:213114901-213237146	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	nsv834527	chr2:213115966-213334308	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1014680	chr2:213142147-213301614	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1004573	chr2:213186537-213365252	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv875811	chr2:213200920-213347104	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv3149	chr2:213204282-213248966	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv584422	chr2:213214303-213270427	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1003694	chr2:213216431-213290523	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11892564	ATIC	cis	parietal	SCAN
rs11892564	MAP2	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:213219200-213227200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:213219200-213233600	Weak transcription	Psoas Muscle	Psoas
3	chr2:213221000-213228600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:213224000-213227200	Enhancers	Fetal Heart	heart
5	chr2:213224200-213227400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:213224600-213228800	Weak transcription	Brain Germinal Matrix	brain
7	chr2:213225000-213228600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:213225200-213226600	Enhancers	HepG2	liver
9	chr2:213225200-213228400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:213225200-213228600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:213225200-213228600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:213225200-213228800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:213225200-213229000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:213225200-213229200	Weak transcription	Fetal Kidney	kidney
15	chr2:213225200-213231600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:213225400-213226600	Enhancers	Brain Anterior Caudate	brain
17	chr2:213225400-213228800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:213225400-213228800	Weak transcription	Brain Angular Gyrus	brain
19	chr2:213225800-213226600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr2:213225800-213226600	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr2:213226000-213226600	Enhancers	Aorta	Aorta
22	chr2:213226200-213226600	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr2:213226400-213228000	Weak transcription	Brain Substantia Nigra	brain
24	chr2:213226400-213228600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:213226400-213228600	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:213226400-213228800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:213226400-213229200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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