Variant report

Variant	rs10790428
Chromosome Location	chr11:121140993-121140994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10219304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1061332	0.90[CHB][hapmap]
rs10750182	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10750183	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10790419	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10790424	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10790432	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10892715	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12419633	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1583124	0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2163281	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59005463	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6589870	0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7115581	0.91[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7115602	0.91[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7119061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7128047	0.87[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7128342	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73005128	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs751417	0.85[CHB][hapmap];0.84[AMR][1000 genomes]
rs7937589	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042295	chr11:121072853-121177079	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
2	nsv898424	chr11:121108865-121206354	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv898425	chr11:121115206-121215237	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv898426	chr11:121136604-121206354	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10790428	SC5DL	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:121138600-121141800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr11:121138800-121141800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:121139000-121142800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:121139200-121142400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:121139600-121143000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:121139800-121141800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr11:121140000-121141000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr11:121140000-121141000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr11:121140600-121141200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:121140800-121141000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr11:121140800-121141000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr11:121140800-121141000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr11:121140800-121141200	Bivalent Enhancer	Brain Anterior Caudate	brain
14	chr11:121140800-121141200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr11:121140800-121141400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:121140800-121141400	Enhancers	Primary hematopoietic stem cells	blood
17	chr11:121140800-121141400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
18	chr11:121140800-121141600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:121140800-121141800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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