Variant report

Variant	rs4959273
Chromosome Location	chr6:475810-475811
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	chr6:474698..477221-chr6:477805..479723,2	K562	blood:
2	chr6:328240..330031-chr6:473438..476214,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11242905	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11242908	0.83[AFR][1000 genomes]
rs13219910	0.88[ASN][1000 genomes]
rs34926067	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4959926	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4959927	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4959928	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6597036	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6597037	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73376966	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73376981	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7745123	0.85[AFR][1000 genomes]
rs925662	0.82[AFR][1000 genomes]
rs9378846	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9392029	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9503977	0.94[ASN][1000 genomes]
rs9503978	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428134	chr6:60001-653718	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv2758034	chr6:60001-775274	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv2759401	chr6:60001-775274	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv531999	chr6:163083-588213	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1067791	chr6:163083-919234	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv497978	chr6:163083-919234	ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv432823	chr6:165391-516350	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv1024273	chr6:170425-510748	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv538028	chr6:170425-510748	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers 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 miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1032462	chr6:170425-766201	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	nsv538029	chr6:170425-766201	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv1034089	chr6:183203-714494	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv538053	chr6:230804-757589	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
14	nsv1016410	chr6:259527-499709	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
15	nsv538055	chr6:259527-499709	Weak transcription Genic enhancers Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
16	nsv533283	chr6:265806-588274	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
17	nsv1032977	chr6:266046-538203	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
18	nsv538064	chr6:266046-538203	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
19	nsv432841	chr6:367109-722716	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
20	nsv883359	chr6:394293-516350	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
21	nsv1034792	chr6:398148-477288	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
22	nsv830569	chr6:402743-573991	Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
23	nsv600781	chr6:403799-833579	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
24	nsv5167	chr6:442174-486632	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
25	nsv948643	chr6:455419-1113509	Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
26	nsv1018244	chr6:460039-476395	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv948744	chr6:472807-1178561	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
28	nsv1023195	chr6:474826-737503	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
29	nsv538070	chr6:474826-737503	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
30	nsv1015678	chr6:474826-866394	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
31	nsv538071	chr6:474826-866394	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4959273	CPNE1	trans	lymphoblastoid	seeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:473400-476200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:474000-485600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:474400-476000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:474600-484600	Weak transcription	Placenta	Placenta
5	chr6:474800-476000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:475000-476000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr6:475200-476200	Enhancers	Primary T cells from cord blood	blood
8	chr6:475400-476000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr6:475400-476000	Enhancers	Dnd41	blood
10	chr6:475400-476200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr6:475400-484600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:475400-484600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:475400-485600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:475600-476000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr6:475600-478800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:475600-484400	Weak transcription	Primary B cells from cord blood	blood
17	chr6:475600-484400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:475600-484400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr6:475600-484400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:475600-484400	Weak transcription	Lung	lung
21	chr6:475600-484600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:475600-484600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:475600-484800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:475600-484800	Weak transcription	Fetal Stomach	stomach
25	chr6:475600-484800	Weak transcription	Left Ventricle	heart
26	chr6:475600-485400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:475600-485400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr6:475600-485600	Weak transcription	Brain Angular Gyrus	brain
29	chr6:475600-485600	Weak transcription	Brain Anterior Caudate	brain
30	chr6:475600-485800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:475600-487600	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:475600-487800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr6:475600-489000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:475600-498600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:475600-511000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:475600-515200	Weak transcription	Brain Germinal Matrix	brain
37	chr6:475800-476000	Bivalent Enhancer	Fetal Lung	lung
38	chr6:475800-477800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:475800-478400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:475800-478800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:475800-478800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr6:475800-478800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr6:475800-478800	Weak transcription	GM12878-XiMat	blood
44	chr6:475800-484600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr6:475800-484600	Weak transcription	Thymus	Thymus
46	chr6:475800-485600	Weak transcription	Fetal Thymus	thymus
47	chr6:475800-488600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr6:475800-489200	Weak transcription	Primary hematopoietic stem cells	blood

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