Variant report

Variant	rs10012379
Chromosome Location	chr4:93228014-93228015
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10009241	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10015916	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10016309	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10032538	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10516906	1.00[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs13121565	0.83[EUR][1000 genomes]
rs13123172	0.88[EUR][1000 genomes]
rs13143394	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13150879	0.83[EUR][1000 genomes]
rs1513454	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1513456	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1513462	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1513467	0.83[EUR][1000 genomes]
rs17019289	0.92[ASN][1000 genomes]
rs17019295	0.91[ASN][1000 genomes]
rs17019316	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17019318	0.91[ASN][1000 genomes]
rs17019329	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17238193	0.83[EUR][1000 genomes]
rs17238679	0.83[EUR][1000 genomes]
rs17317393	0.83[EUR][1000 genomes]
rs17619771	0.83[EUR][1000 genomes]
rs1877598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2175767	0.82[EUR][1000 genomes]
rs28396937	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429309	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28550894	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28864996	0.86[ASN][1000 genomes]
rs34742978	0.83[EUR][1000 genomes]
rs35214260	0.88[EUR][1000 genomes]
rs35358234	0.88[EUR][1000 genomes]
rs36116627	0.83[EUR][1000 genomes]
rs36123040	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62310971	0.86[EUR][1000 genomes]
rs62310990	0.89[EUR][1000 genomes]
rs62310993	0.89[EUR][1000 genomes]
rs62310994	0.88[EUR][1000 genomes]
rs62311001	0.83[EUR][1000 genomes]
rs6812781	0.90[ASN][1000 genomes]
rs6824860	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6830966	0.82[ASN][1000 genomes]
rs6848132	0.83[EUR][1000 genomes]
rs6848674	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7692631	0.94[ASN][1000 genomes]
rs951961	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs951962	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9884958	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9990511	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.94[MKK][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530154	chr4:92396539-93359983	Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv999701	chr4:92518040-93233556	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv537180	chr4:92518040-93233556	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1009960	chr4:92747531-93389054	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv470056	chr4:92837584-93322977	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv461587	chr4:92837584-93376231	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv594866	chr4:92837584-93376231	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv948712	chr4:93007985-93740409	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv879603	chr4:93053028-93276174	ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv879604	chr4:93064187-93287744	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv830007	chr4:93101912-93317656	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv594868	chr4:93190198-93391251	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv998246	chr4:93198845-93350325	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	esv1835393	chr4:93222515-93276174	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:93224000-93228600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:93224400-93228400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr4:93224400-93229200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr4:93224600-93229600	Active TSS	Brain Cingulate Gyrus	brain
5	chr4:93224600-93229800	Active TSS	Brain Anterior Caudate	brain
6	chr4:93227600-93229200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:93227600-93229200	Weak transcription	Brain Substantia Nigra	brain
8	chr4:93227600-93240600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:93227800-93228200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr4:93227800-93228400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:93227800-93228600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr4:93227800-93229200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr4:93227800-93229400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:93228000-93228400	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr4:93228000-93228400	Enhancers	Brain Angular Gyrus	brain
16	chr4:93228000-93229000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr4:93228000-93229000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:93228000-93229000	Weak transcription	Fetal Brain Female	brain
19	chr4:93228000-93230000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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