Variant report

Variant	rs6545389
Chromosome Location	chr2:54386901-54386902
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	chr2:54341229..54346589-chr2:54385136..54390434,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10208233	0.82[ASN][1000 genomes]
rs1058320	0.85[CEU][hapmap]
rs1075265	0.85[CEU][hapmap]
rs11125523	0.87[ASN][1000 genomes]
rs1118618	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1877906	0.83[EUR][1000 genomes]
rs2048749	0.81[EUR][1000 genomes]
rs2112124	0.82[EUR][1000 genomes]
rs2287642	0.85[CEU][hapmap]
rs4671872	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4671889	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6545379	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs6545388	0.92[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs6724389	1.00[CHB][hapmap]
rs7566894	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7569743	0.82[EUR][1000 genomes]
rs805309	0.83[CEU][hapmap]
rs918357	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs929734	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1007731	chr2:54331179-54452329	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
10	nsv535723	chr2:54331179-54452329	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	nsv874148	chr2:54344325-54432222	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	nsv1000652	chr2:54345892-54469703	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv1003889	chr2:54347750-54424601	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv1011433	chr2:54351145-54424601	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv1012230	chr2:54351988-54422959	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv874149	chr2:54358517-54432222	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6545389	PNPT1	cis	cerebellum	SCAN
rs6545389	ACYP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54343400-54388600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:54352200-54411400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:54361400-54389800	Weak transcription	Lung	lung
4	chr2:54362000-54416400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr2:54362200-54391400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:54362200-54411200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:54362800-54387000	Weak transcription	Brain Angular Gyrus	brain
8	chr2:54366400-54389200	Weak transcription	Fetal Stomach	stomach
9	chr2:54366400-54391200	Weak transcription	Spleen	Spleen
10	chr2:54366400-54397200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:54366600-54409600	Weak transcription	Psoas Muscle	Psoas
12	chr2:54367400-54416600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:54369600-54416600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:54371400-54387000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:54377400-54391200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:54377800-54387000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:54377800-54387000	Weak transcription	HSMMtube	muscle
18	chr2:54380600-54429200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr2:54380600-54434400	Weak transcription	Ovary	ovary
20	chr2:54380800-54387000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:54382200-54389200	Weak transcription	Fetal Heart	heart
22	chr2:54382800-54387000	Weak transcription	Aorta	Aorta
23	chr2:54382800-54387000	Weak transcription	Brain Anterior Caudate	brain
24	chr2:54382800-54387800	Weak transcription	Right Ventricle	heart
25	chr2:54382800-54389200	Weak transcription	Fetal Lung	lung
26	chr2:54382800-54389400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:54382800-54394800	Weak transcription	Fetal Brain Male	brain
28	chr2:54382800-54414600	Weak transcription	Fetal Intestine Small	intestine
29	chr2:54383000-54387000	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:54383000-54389200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:54383000-54389400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:54383000-54393200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:54383200-54390400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:54383800-54393000	Weak transcription	Primary B cells from cord blood	blood
35	chr2:54384000-54389600	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:54385200-54390600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:54385800-54415800	Weak transcription	Left Ventricle	heart
38	chr2:54386000-54388600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr2:54386000-54389800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr2:54386400-54389200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:54386600-54390800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:54386800-54387200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:54386800-54387200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:54386800-54387400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:54386800-54387600	Strong transcription	Adipose Nuclei	Adipose
46	chr2:54386800-54387800	Strong transcription	Liver	Liver
47	chr2:54386800-54387800	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:54386800-54387800	Enhancers	K562	blood
49	chr2:54386800-54388000	Enhancers	Brain Cingulate Gyrus	brain
50	chr2:54386800-54388400	Enhancers	Brain Inferior Temporal Lobe	brain

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