Variant report

Variant	rs13120905
Chromosome Location	chr4:15612288-15612289
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15606192..15608992-chr4:15609587..15612464,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10008376	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10008975	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10214	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728084	0.88[EUR][1000 genomes]
rs12499412	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12500587	0.91[EUR][1000 genomes]
rs12500770	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12512883	0.89[EUR][1000 genomes]
rs12644655	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12651550	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13110674	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13129739	0.87[EUR][1000 genomes]
rs13142069	0.84[AFR][1000 genomes]
rs13147590	0.96[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35414597	0.88[EUR][1000 genomes]
rs4235379	0.92[EUR][1000 genomes]
rs4270584	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4333182	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4453929	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4470622	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4524378	0.93[EUR][1000 genomes]
rs4557256	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616746	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4631041	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4698402	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698404	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698406	0.92[EUR][1000 genomes]
rs4698407	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698409	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61021642	0.91[EUR][1000 genomes]
rs6414765	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414767	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6414768	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6449153	0.95[EUR][1000 genomes]
rs6449161	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6850169	0.83[EUR][1000 genomes]
rs6850422	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7438356	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662032	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7684446	0.84[AFR][1000 genomes]
rs7685083	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7687003	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7688984	0.95[EUR][1000 genomes]
rs7696127	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9997068	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3464781	chr4:15607348-15613955	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3464782	chr4:15607355-15613914	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3464780	chr4:15607407-15613891	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3464783	chr4:15607421-15613890	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv518830	chr4:15610771-15672200	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13120905	FBXL5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
2	chr4:15550000-15617800	Weak transcription	Thymus	Thymus
3	chr4:15565400-15612600	Weak transcription	Brain Substantia Nigra	brain
4	chr4:15565400-15621400	Weak transcription	Esophagus	oesophagus
5	chr4:15568400-15655600	Weak transcription	Gastric	stomach
6	chr4:15575200-15618000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:15587200-15612600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:15589800-15621400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:15590000-15615600	Weak transcription	Lung	lung
10	chr4:15590600-15626400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:15593800-15621200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:15594600-15617800	Weak transcription	Right Ventricle	heart
13	chr4:15595400-15614000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:15596000-15612800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr4:15596600-15616400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:15597200-15620600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr4:15600600-15620800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:15600800-15653000	Weak transcription	Colonic Mucosa	Colon
19	chr4:15601000-15651600	Weak transcription	Small Intestine	intestine
20	chr4:15602000-15626000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr4:15602200-15621200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:15602400-15612600	Weak transcription	Brain Angular Gyrus	brain
23	chr4:15602400-15615600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:15602600-15615800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:15602600-15655600	Weak transcription	Pancreas	Pancrea
26	chr4:15603000-15624400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr4:15603800-15626800	Weak transcription	NHLF	lung
28	chr4:15604200-15617800	Weak transcription	Spleen	Spleen
29	chr4:15604600-15612600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr4:15604600-15615600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:15604600-15615600	Weak transcription	Aorta	Aorta
32	chr4:15604600-15615600	Weak transcription	Fetal Intestine Small	intestine
33	chr4:15604600-15615600	Weak transcription	Fetal Stomach	stomach
34	chr4:15604800-15612600	Weak transcription	NHEK	skin
35	chr4:15604800-15615600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr4:15604800-15615600	Weak transcription	Ovary	ovary
37	chr4:15604800-15617800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:15605200-15612800	Weak transcription	Placenta	Placenta
39	chr4:15605200-15615600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:15605400-15615600	Weak transcription	Fetal Brain Female	brain
41	chr4:15605400-15615600	Weak transcription	Fetal Muscle Leg	muscle
42	chr4:15605400-15625800	Weak transcription	HMEC	breast
43	chr4:15605600-15620400	Weak transcription	Colon Smooth Muscle	Colon
44	chr4:15605600-15624400	Weak transcription	K562	blood
45	chr4:15605800-15612600	Weak transcription	Brain Anterior Caudate	brain
46	chr4:15605800-15615600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:15605800-15618400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:15605800-15621000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr4:15605800-15650200	Weak transcription	Stomach Mucosa	stomach
50	chr4:15606000-15612600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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