Variant report

Variant	rs3898027
Chromosome Location	chr10:23165066-23165067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10082509	0.96[ASN][1000 genomes]
rs10082523	0.95[ASN][1000 genomes]
rs10508654	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs10828355	0.94[ASN][1000 genomes]
rs11013153	0.85[EUR][1000 genomes]
rs11013164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12246800	0.98[ASN][1000 genomes]
rs12261989	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12266797	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12266919	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12267652	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12571972	0.85[EUR][1000 genomes]
rs16922725	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs16922749	0.85[EUR][1000 genomes]
rs16922762	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16922768	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1934779	0.90[EUR][1000 genomes]
rs7078414	0.85[EUR][1000 genomes]
rs73600551	0.98[ASN][1000 genomes]
rs7894365	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7906311	0.96[ASN][1000 genomes]
rs7914616	0.98[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	esv2764013	chr10:23087298-23239345	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv894966	chr10:23090535-23202522	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3898027	COL5A2	trans	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:23161400-23165400	Enhancers	Brain Substantia Nigra	brain
2	chr10:23162400-23167400	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr10:23162600-23165400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr10:23162800-23166000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr10:23162800-23166400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr10:23163200-23165800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr10:23163400-23165200	Enhancers	Brain Hippocampus Middle	brain
8	chr10:23163400-23166200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr10:23163400-23166200	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr10:23163400-23169600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr10:23163800-23165200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr10:23164400-23165200	Enhancers	Fetal Intestine Small	intestine
13	chr10:23164600-23165200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr10:23164600-23165200	Enhancers	Brain Angular Gyrus	brain
15	chr10:23164800-23165400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr10:23164800-23165400	Enhancers	Brain Germinal Matrix	brain
17	chr10:23164800-23165800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr10:23164800-23165800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr10:23164800-23169600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr10:23165000-23165200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr10:23165000-23165200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr10:23165000-23165200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr10:23165000-23165400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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