Variant report

Variant	rs41270305
Chromosome Location	chr5:50118250-50118251
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	chr5:50111976..50114823-chr5:50117408..50119035,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10052372	0.90[EUR][1000 genomes]
rs11950506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11952107	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11954064	0.94[AMR][1000 genomes]
rs11955651	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11955934	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11959326	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13155662	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13156735	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13157079	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13159045	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13159239	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13161225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13162738	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13163470	0.94[EUR][1000 genomes]
rs13163802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13166819	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13169153	0.94[EUR][1000 genomes]
rs13171248	0.81[AMR][1000 genomes]
rs13174498	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13176737	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13181031	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13181117	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13183910	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13186653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13189183	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13190144	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16886309	0.94[EUR][1000 genomes]
rs1968637	0.81[AMR][1000 genomes]
rs2354531	0.81[AMR][1000 genomes]
rs34183555	0.83[AMR][1000 genomes]
rs34264957	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34414061	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34677483	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34758774	0.85[EUR][1000 genomes]
rs34827507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34855203	0.81[EUR][1000 genomes]
rs35128589	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35210389	1.00[AMR][1000 genomes]
rs35347195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35473824	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6859621	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6880398	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6883701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6888271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6888315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6892149	0.89[AMR][1000 genomes]
rs71615975	0.83[AMR][1000 genomes]
rs71615978	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71615981	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71615983	0.94[EUR][1000 genomes]
rs71615984	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71615986	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71615988	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71615990	0.98[EUR][1000 genomes]
rs71615991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7717073	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7723395	0.81[AMR][1000 genomes]
rs7726225	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7733931	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1016237	chr5:49986171-50118816	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv537761	chr5:49986171-50118816	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41270305	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50056800-50126400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:50064000-50126800	Weak transcription	Osteobl	bone
3	chr5:50071600-50138200	Weak transcription	Placenta	Placenta
4	chr5:50078200-50140000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:50085400-50123800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr5:50085400-50136200	Weak transcription	Thymus	Thymus
7	chr5:50091200-50118800	Weak transcription	Spleen	Spleen
8	chr5:50091200-50123800	Weak transcription	Fetal Thymus	thymus
9	chr5:50091200-50124800	Weak transcription	Esophagus	oesophagus
10	chr5:50091200-50130400	Weak transcription	Pancreas	Pancrea
11	chr5:50091200-50133600	Weak transcription	Lung	lung
12	chr5:50091200-50136000	Weak transcription	Gastric	stomach
13	chr5:50091200-50140600	Weak transcription	Small Intestine	intestine
14	chr5:50091400-50124000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:50091800-50123400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:50094000-50123800	Weak transcription	HMEC	breast
17	chr5:50095800-50123400	Weak transcription	Fetal Lung	lung
18	chr5:50096000-50132200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:50099400-50123800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:50100000-50118600	Weak transcription	Aorta	Aorta
21	chr5:50100200-50139400	Weak transcription	Ovary	ovary
22	chr5:50100400-50118800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr5:50100400-50123800	Weak transcription	Left Ventricle	heart
24	chr5:50102400-50118400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:50104600-50129400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:50104600-50136200	Weak transcription	NHEK	skin
27	chr5:50104800-50123600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr5:50107800-50118800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:50108000-50135000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:50108200-50142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:50109400-50124000	Weak transcription	Fetal Intestine Large	intestine
32	chr5:50109400-50141800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr5:50109600-50129000	Strong transcription	Dnd41	blood
34	chr5:50109800-50134400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:50109800-50136400	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr5:50110000-50141800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr5:50110400-50128000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
38	chr5:50110400-50133400	Strong transcription	Primary B cells from cord blood	blood
39	chr5:50110400-50143400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr5:50110400-50143600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:50110600-50134600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:50110800-50132000	Weak transcription	Brain Substantia Nigra	brain
43	chr5:50110800-50133400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr5:50110800-50140200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr5:50111000-50140800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr5:50111200-50121000	Strong transcription	Primary B cells from peripheral blood	blood
47	chr5:50111200-50141600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr5:50111400-50124800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr5:50111400-50127000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr5:50111800-50121800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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