Variant report

Variant	rs6883701
Chromosome Location	chr5:50100205-50100206
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	chr16:1155873..1156568-chr5:50099716..50100332,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10052372	0.96[EUR][1000 genomes]
rs11950506	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11952107	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11954064	0.94[AMR][1000 genomes]
rs11955651	0.85[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11955934	0.88[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11959326	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13155662	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13156735	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13157079	0.88[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13159045	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13159239	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13161225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13162738	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13163470	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs13163802	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13166819	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13169153	1.00[EUR][1000 genomes]
rs13171248	0.81[AMR][1000 genomes]
rs13174498	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13176737	0.88[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13181031	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13181117	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13183910	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13186653	0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13189183	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13190144	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16886309	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs1968637	0.81[AMR][1000 genomes]
rs2354531	0.81[AMR][1000 genomes]
rs34183555	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34264957	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34414061	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34677483	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34758774	0.90[EUR][1000 genomes]
rs34827507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34855203	0.87[EUR][1000 genomes]
rs35128589	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35210389	1.00[AMR][1000 genomes]
rs35347195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35473824	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35596019	1.00[AMR][1000 genomes]
rs41270305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6859621	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6880398	0.88[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6888271	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6888315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6892149	0.88[CEU][hapmap];0.89[AMR][1000 genomes]
rs71615975	0.83[AMR][1000 genomes]
rs71615978	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71615981	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71615983	1.00[EUR][1000 genomes]
rs71615984	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71615986	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71615988	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71615990	0.96[EUR][1000 genomes]
rs71615991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7717073	0.88[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7723395	0.81[AMR][1000 genomes]
rs7726225	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7733931	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	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
3	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
rs6883701	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 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	chr5:50071400-50108000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr5:50071600-50138200	Weak transcription	Placenta	Placenta
5	chr5:50078200-50140000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:50083200-50116800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:50085400-50123800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:50085400-50136200	Weak transcription	Thymus	Thymus
9	chr5:50090600-50100600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:50091200-50103600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:50091200-50104000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:50091200-50113800	Weak transcription	Fetal Stomach	stomach
13	chr5:50091200-50116200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:50091200-50118800	Weak transcription	Spleen	Spleen
15	chr5:50091200-50123800	Weak transcription	Fetal Thymus	thymus
16	chr5:50091200-50124800	Weak transcription	Esophagus	oesophagus
17	chr5:50091200-50130400	Weak transcription	Pancreas	Pancrea
18	chr5:50091200-50133600	Weak transcription	Lung	lung
19	chr5:50091200-50136000	Weak transcription	Gastric	stomach
20	chr5:50091200-50140600	Weak transcription	Small Intestine	intestine
21	chr5:50091400-50101600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:50091400-50124000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr5:50091800-50104000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:50091800-50123400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:50093200-50112200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr5:50094000-50111200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr5:50094000-50123800	Weak transcription	HMEC	breast
28	chr5:50094200-50111600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:50095600-50103200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:50095800-50114800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:50095800-50123400	Weak transcription	Fetal Lung	lung
32	chr5:50096000-50132200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr5:50097400-50100400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:50098000-50100400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:50098400-50108000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr5:50099000-50100800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:50099200-50100400	Strong transcription	Adipose Nuclei	Adipose
38	chr5:50099200-50107000	Strong transcription	Primary B cells from cord blood	blood
39	chr5:50099200-50108200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr5:50099200-50112000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:50099400-50100400	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:50099400-50100600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:50099400-50101600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr5:50099400-50101600	Weak transcription	Dnd41	blood
45	chr5:50099400-50101800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr5:50099400-50104600	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr5:50099400-50115600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:50099400-50123800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:50099600-50100400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr5:50099600-50102400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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