Variant report

Variant	rs6893317
Chromosome Location	chr5:49714391-49714392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:49713946..49715979-chr5:49717619..49720467,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs13154421	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs13158256	0.97[EUR][1000 genomes]
rs13169411	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13174803	0.95[EUR][1000 genomes]
rs13185634	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13189140	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17192300	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17192503	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17800685	0.93[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1962207	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34573392	0.82[AMR][1000 genomes]
rs34982640	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35005767	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35220247	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs35319490	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs35647517	0.97[EUR][1000 genomes]
rs35703604	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35831659	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36108557	0.82[EUR][1000 genomes]
rs3860733	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58931923	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs61133464	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71631461	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71631463	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71631464	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71631467	1.00[EUR][1000 genomes]
rs71631474	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs71631475	0.80[EUR][1000 genomes]
rs7709512	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1032003	chr5:49455624-49881491	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1023981	chr5:49584188-49871537	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv537757	chr5:49584188-49871537	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv916441	chr5:49584313-49831223	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6893317	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49682000-49719000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:49690200-49723600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr5:49697000-49723400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:49697400-49723400	Weak transcription	HSMM	muscle
5	chr5:49697600-49719000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:49697600-49721600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:49703200-49719000	Weak transcription	HMEC	breast
8	chr5:49703200-49724600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr5:49703200-49727000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:49705400-49715800	Weak transcription	Fetal Intestine Large	intestine
11	chr5:49707200-49715000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr5:49709400-49715000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr5:49709600-49715000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr5:49709600-49716800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:49709800-49715000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr5:49709800-49715600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr5:49710000-49714600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr5:49710000-49715000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:49710000-49715200	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr5:49712200-49715400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:49712200-49718200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:49712200-49718600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr5:49712600-49714800	Enhancers	Primary T cells from cord blood	blood
24	chr5:49712600-49715000	Enhancers	Dnd41	blood
25	chr5:49712600-49716000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr5:49712800-49716200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr5:49713000-49716200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr5:49713000-49719600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr5:49713000-49722000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr5:49713000-49722600	Weak transcription	Fetal Thymus	thymus
31	chr5:49713000-49725800	Weak transcription	Small Intestine	intestine
32	chr5:49713200-49714600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:49713200-49715400	Weak transcription	Primary B cells from cord blood	blood
34	chr5:49713200-49716200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr5:49714000-49714800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood

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