Variant report

Variant	rs11747742
Chromosome Location	chr5:178055638-178055639
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178052822..178055819-chr5:178156143..178158096,2	MCF-7	breast:
2	chr5:178052987..178056050-chr5:178056072..178058258,3	MCF-7	breast:
3	chr5:178054261..178056030-chr5:178057503..178059124,2	MCF-7	breast:
4	chr5:178054847..178056678-chr5:178067285..178069085,2	K562	blood:
5	chr5:178054153..178056905-chr5:178057584..178060537,3	K562	blood:

Variant related genes	Relation type
ENSG00000113240	Chromatin interaction
ENSG00000169131	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10063220	0.83[ASN][1000 genomes]
rs11249553	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11249554	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11249556	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11737903	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740194	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746942	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12514311	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12518589	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13155255	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13156622	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs262027	0.85[CHB][hapmap]
rs35460909	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35522922	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36008351	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3925518	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs4079110	0.82[ASN][1000 genomes]
rs4587090	0.82[ASN][1000 genomes]
rs4976738	0.83[ASN][1000 genomes]
rs4976800	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs501721	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs519984	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs530542	0.91[EUR][1000 genomes]
rs555417	0.88[JPT][hapmap];0.81[YRI][hapmap]
rs574103	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs576097	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs584415	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs596780	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs602019	0.87[ASN][1000 genomes]
rs602451	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs628857	0.92[CEU][hapmap]
rs643936	0.91[EUR][1000 genomes]
rs649585	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6863876	0.81[ASN][1000 genomes]
rs6865775	0.83[ASN][1000 genomes]
rs6882079	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6883747	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs6886390	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6890632	0.83[ASN][1000 genomes]
rs721144	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7700943	0.82[CEU][hapmap]
rs7702727	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7724406	0.82[CEU][hapmap]
rs7732660	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs9329045	0.83[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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11747742	CLK4	Cis_1M	lymphoblastoid	RTeQTL
rs11747742	CLK4	cis	normal skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178054600-178055800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:178054600-178057200	Enhancers	HepG2	liver
3	chr5:178054600-178057400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:178054600-178057400	Weak transcription	K562	blood
5	chr5:178054600-178057600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:178054600-178057800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:178054600-178058800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:178054600-178059200	Weak transcription	Right Atrium	heart
9	chr5:178054600-178061600	Weak transcription	HMEC	breast
10	chr5:178054800-178057200	Weak transcription	NHEK	skin
11	chr5:178054800-178057400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:178054800-178057400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:178054800-178057400	Weak transcription	Hela-S3	cervix
14	chr5:178054800-178057400	Weak transcription	NH-A	brain
15	chr5:178054800-178057400	Weak transcription	Osteobl	bone
16	chr5:178054800-178058000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:178055000-178057400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr5:178055000-178057800	Weak transcription	Primary B cells from cord blood	blood
19	chr5:178055200-178056000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell

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