Variant report

Variant	rs4757717
Chromosome Location	chr11:18795058-18795059
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4075664	0.90[CHB][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs4274187	0.86[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4372421	0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[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	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv525452	chr11:18735947-18802503	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4757717	SERGEF	cis	parietal	SCAN
rs4757717	CALCB	cis	cerebellum	SCAN
rs4757717	NELL1	cis	parietal	SCAN
rs4757717	GTF2H1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18783000-18801800	Weak transcription	Spleen	Spleen
2	chr11:18784000-18808000	Weak transcription	Fetal Brain Female	brain
3	chr11:18790800-18811400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:18793600-18809000	Weak transcription	Brain Angular Gyrus	brain
5	chr11:18793800-18795200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:18793800-18796000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr11:18794000-18795400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr11:18794000-18795400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:18794000-18795600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:18794000-18796200	Enhancers	Fetal Muscle Trunk	muscle
11	chr11:18794200-18795400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr11:18794200-18795600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr11:18794200-18795600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
14	chr11:18794400-18795200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
15	chr11:18794400-18796000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr11:18794600-18795200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr11:18794600-18795200	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr11:18794600-18811800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:18795000-18795400	Enhancers	Brain Anterior Caudate	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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