Variant report

Variant	rs17016123
Chromosome Location	chr4:143355338-143355339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:143355305-143355927	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:143348784..143353302-chr4:143354047..143356332,5	MCF-7	breast:
2	chr4:143351692..143359150-chr4:143392769..143399702,12	MCF-7	breast:
3	chr4:143355259..143357317-chr4:143383391..143385106,2	MCF-7	breast:

Variant related genes	Relation type
INPP4B	TF binding region
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10519644	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs11930321	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs11944462	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs11944503	0.84[EUR][1000 genomes]
rs12499785	0.87[EUR][1000 genomes]
rs12500699	0.90[EUR][1000 genomes]
rs2130251	0.87[EUR][1000 genomes]
rs2130252	0.85[EUR][1000 genomes]
rs2171756	0.87[EUR][1000 genomes]
rs28555074	0.87[EUR][1000 genomes]
rs28588752	0.87[EUR][1000 genomes]
rs3775704	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4435818	0.87[EUR][1000 genomes]
rs4476678	0.88[EUR][1000 genomes]
rs4551010	0.87[EUR][1000 genomes]
rs4566727	0.90[EUR][1000 genomes]
rs61515079	0.90[EUR][1000 genomes]
rs66511868	0.87[EUR][1000 genomes]
rs66537547	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs66941440	0.87[EUR][1000 genomes]
rs67001118	0.87[EUR][1000 genomes]
rs67013221	0.87[EUR][1000 genomes]
rs67111439	0.87[EUR][1000 genomes]
rs67440355	0.87[EUR][1000 genomes]
rs67947007	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6820234	0.90[EUR][1000 genomes]
rs6829034	0.88[EUR][1000 genomes]
rs6839769	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6851331	0.90[EUR][1000 genomes]
rs6854342	0.88[EUR][1000 genomes]
rs72724531	0.81[EUR][1000 genomes]
rs72724534	0.81[EUR][1000 genomes]
rs72941192	0.81[EUR][1000 genomes]
rs72944948	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs931421	1.00[CEU][hapmap];1.00[JPT][hapmap]

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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17016123	IL15	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143338600-143366600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:143339000-143355400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr4:143350000-143355400	Weak transcription	Fetal Heart	heart
4	chr4:143350000-143356200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:143350000-143356200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:143350200-143356000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr4:143351200-143364800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:143351200-143371200	Weak transcription	Pancreas	Pancrea
9	chr4:143351600-143356200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:143352400-143356800	Weak transcription	Left Ventricle	heart
11	chr4:143352400-143359400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:143353000-143360800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:143354000-143355800	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr4:143354400-143355800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:143354600-143356200	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr4:143354800-143355800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr4:143354800-143356000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr4:143355000-143355600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:143355200-143356800	Weak transcription	Thymus	Thymus

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