Variant report

Variant	rs16902639
Chromosome Location	chr5:35938994-35938995
allele	C/G
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	PBX3	chr5:35938662-35939081	SK-N-SH	brain:	n/a	chr5:35938832-35938841 chr5:35938849-35938858 chr5:35938836-35938856
2	RFX5	chr5:35938752-35939002	GM12878	blood:	n/a	chr5:35938832-35938841
3	NFYB	chr5:35938601-35939012	GM12878	blood:	n/a	chr5:35938833-35938845 chr5:35938829-35938844 chr5:35938831-35938846 chr5:35938832-35938842
4	RFX5	chr5:35938545-35939237	IMR90	lung:	n/a	chr5:35938832-35938841
5	SP1	chr5:35938566-35939087	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD2	chr5:35938636-35939048	H1-hESC	embryonic stem cell:	n/a	n/a
7	PBX3	chr5:35938657-35939128	SK-N-SH	brain:	n/a	chr5:35938832-35938841 chr5:35938849-35938858 chr5:35938836-35938856
8	RFX5	chr5:35938550-35939233	SK-N-SH	brain:	n/a	chr5:35938832-35938841
9	RFX5	chr5:35938693-35939026	H1-hESC	embryonic stem cell:	n/a	chr5:35938832-35938841
10	RFX5	chr5:35938720-35939041	Hela-S3	cervix:	n/a	chr5:35938832-35938841
11	FOXA1	chr5:35938681-35939043	T-47D	breast:	n/a	n/a
12	MAX	chr5:35938724-35938994	H1-hESC	embryonic stem cell:	n/a	n/a
13	SP2	chr5:35938601-35939013	H1-hESC	embryonic stem cell:	n/a	chr5:35938835-35938858
14	RFX5	chr5:35938810-35939004	HepG2	liver:	n/a	chr5:35938832-35938841
15	SP2	chr5:35938554-35939050	H1-hESC	embryonic stem cell:	n/a	chr5:35938835-35938858
16	SP1	chr5:35938559-35939090	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IL7R-1	chr5:35938924-35939026	XLOC_004337
2	lnc-IL7R-1	chr5:35938903-35939026	NR_104630
3	lnc-IL7R-1	chr5:35938923-35939026	NONHSAT101017

Variant related genes	Relation type
CAPSL	TF binding region

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10041865	1.00[EUR][1000 genomes]
rs10058723	1.00[EUR][1000 genomes]
rs10058960	1.00[EUR][1000 genomes]
rs10077553	1.00[EUR][1000 genomes]
rs10079269	1.00[EUR][1000 genomes]
rs10079517	1.00[EUR][1000 genomes]
rs10491432	1.00[EUR][1000 genomes]
rs10491433	1.00[EUR][1000 genomes]
rs11567717	1.00[EUR][1000 genomes]
rs11567730	1.00[EUR][1000 genomes]
rs11567764	1.00[EUR][1000 genomes]
rs1374015	1.00[EUR][1000 genomes]
rs1494570	1.00[EUR][1000 genomes]
rs16902514	1.00[EUR][1000 genomes]
rs16902535	1.00[EUR][1000 genomes]
rs16902557	1.00[EUR][1000 genomes]
rs16902562	1.00[EUR][1000 genomes]
rs16902592	1.00[EUR][1000 genomes]
rs16902593	1.00[EUR][1000 genomes]
rs16902594	1.00[EUR][1000 genomes]
rs16902638	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16902643	1.00[EUR][1000 genomes]
rs16902650	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs16902651	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs16902667	0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs16902670	1.00[EUR][1000 genomes]
rs16902682	1.00[EUR][1000 genomes]
rs28756345	1.00[EUR][1000 genomes]
rs56053392	1.00[EUR][1000 genomes]
rs56169453	1.00[EUR][1000 genomes]
rs56276485	1.00[EUR][1000 genomes]
rs56665523	1.00[EUR][1000 genomes]
rs56773364	1.00[EUR][1000 genomes]
rs57273729	1.00[EUR][1000 genomes]
rs57498894	1.00[EUR][1000 genomes]
rs57579833	1.00[EUR][1000 genomes]
rs58168401	1.00[EUR][1000 genomes]
rs58457055	1.00[EUR][1000 genomes]
rs58872016	1.00[EUR][1000 genomes]
rs59714026	1.00[EUR][1000 genomes]
rs6451222	1.00[EUR][1000 genomes]
rs6861184	1.00[EUR][1000 genomes]
rs6864736	1.00[EUR][1000 genomes]
rs6875303	1.00[EUR][1000 genomes]
rs6876261	1.00[EUR][1000 genomes]
rs6881919	1.00[EUR][1000 genomes]
rs6894309	1.00[EUR][1000 genomes]
rs73076116	1.00[EUR][1000 genomes]
rs73076118	1.00[EUR][1000 genomes]
rs73076126	1.00[EUR][1000 genomes]
rs73076137	1.00[EUR][1000 genomes]
rs73076149	1.00[EUR][1000 genomes]
rs73076151	1.00[EUR][1000 genomes]
rs73076155	1.00[EUR][1000 genomes]
rs73076161	1.00[EUR][1000 genomes]
rs73076166	1.00[EUR][1000 genomes]
rs73076168	1.00[EUR][1000 genomes]
rs73076171	1.00[EUR][1000 genomes]
rs73076172	1.00[EUR][1000 genomes]
rs73076173	1.00[EUR][1000 genomes]
rs73076178	1.00[EUR][1000 genomes]
rs73076180	1.00[EUR][1000 genomes]
rs73076197	1.00[EUR][1000 genomes]
rs73076199	1.00[EUR][1000 genomes]
rs73078005	1.00[EUR][1000 genomes]
rs73078010	1.00[EUR][1000 genomes]
rs73078011	1.00[EUR][1000 genomes]
rs73078024	1.00[EUR][1000 genomes]
rs73086251	1.00[EUR][1000 genomes]
rs73086261	1.00[EUR][1000 genomes]
rs73086281	1.00[EUR][1000 genomes]
rs73086282	1.00[EUR][1000 genomes]
rs73086302	1.00[EUR][1000 genomes]
rs73088209	1.00[EUR][1000 genomes]
rs73088244	1.00[EUR][1000 genomes]
rs73090209	1.00[EUR][1000 genomes]
rs73090222	1.00[EUR][1000 genomes]
rs73090239	1.00[EUR][1000 genomes]
rs73090241	1.00[EUR][1000 genomes]
rs73090248	1.00[EUR][1000 genomes]
rs73090257	1.00[EUR][1000 genomes]
rs73090276	1.00[EUR][1000 genomes]
rs73090284	1.00[EUR][1000 genomes]
rs73090289	1.00[EUR][1000 genomes]
rs73090291	1.00[EUR][1000 genomes]
rs73090295	1.00[EUR][1000 genomes]
rs73090298	1.00[EUR][1000 genomes]
rs73092011	1.00[EUR][1000 genomes]
rs73092033	1.00[EUR][1000 genomes]
rs73092034	1.00[EUR][1000 genomes]
rs73092092	1.00[EUR][1000 genomes]
rs73092100	1.00[EUR][1000 genomes]
rs73094009	1.00[EUR][1000 genomes]
rs73094019	1.00[EUR][1000 genomes]
rs73094022	1.00[EUR][1000 genomes]
rs7701519	1.00[EUR][1000 genomes]
rs7704710	1.00[EUR][1000 genomes]
rs7708334	1.00[EUR][1000 genomes]
rs7710405	1.00[EUR][1000 genomes]
rs7714297	1.00[EUR][1000 genomes]
rs7720394	1.00[EUR][1000 genomes]
rs7724777	1.00[EUR][1000 genomes]
rs9292610	1.00[EUR][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	nsv471011	chr5:35861068-36003217	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv830261	chr5:35863084-36018048	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1025695	chr5:35902486-36036934	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35938200-35939000	Active TSS	Brain Anterior Caudate	brain
2	chr5:35938200-35939200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:35938400-35939000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr5:35938400-35939400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr5:35938600-35939000	Enhancers	Duodenum Smooth Muscle	Duodenum
6	chr5:35938600-35939000	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr5:35938600-35939200	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr5:35938600-35939200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:35938600-35939200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:35938600-35939200	Enhancers	Brain Cingulate Gyrus	brain
11	chr5:35938600-35939200	Enhancers	Fetal Stomach	stomach
12	chr5:35938600-35939400	Enhancers	Fetal Lung	lung
13	chr5:35938600-35939600	Enhancers	Fetal Thymus	thymus
14	chr5:35938600-35939600	Enhancers	Thymus	Thymus
15	chr5:35938800-35939200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:35938800-35939200	Enhancers	Fetal Kidney	kidney

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