Variant report

Variant	rs10219304
Chromosome Location	chr11:121127685-121127686
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	chr11:121123220..121124727-chr11:121126741..121128894,2	MCF-7	breast:
2	chr11:121126834..121128836-chr11:121162575..121164973,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109929	Chromatin interaction

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

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

rs_ID	r²[population]
rs1061332	0.90[CHB][hapmap]
rs10750182	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10750183	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10790419	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10790424	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10790428	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10790432	0.86[EUR][1000 genomes]
rs10892715	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12419633	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1583124	0.91[CEU][hapmap];0.95[CHB][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2163281	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs59005463	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6589870	0.91[CEU][hapmap];0.95[CHB][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7115581	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes]
rs7115602	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes]
rs7119061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128047	0.87[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7128342	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73005128	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs751417	0.85[CHB][hapmap]
rs7937589	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10219304	SC5DL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:121124800-121128200	Weak transcription	NHEK	skin
2	chr11:121125000-121128200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:121125000-121128200	Weak transcription	HMEC	breast
4	chr11:121125000-121136000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:121125600-121128400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:121126600-121128000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:121126800-121127800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr11:121126800-121128600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr11:121127200-121128000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:121127200-121128200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr11:121127600-121129400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:121127600-121129400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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