Variant report

Variant	rs2354149
Chromosome Location	chr5:1628823-1628824
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11747600	0.89[ASN][1000 genomes]
rs12658097	0.84[ASN][1000 genomes]
rs12658927	0.87[ASN][1000 genomes]
rs13158448	0.87[ASN][1000 genomes]
rs13181671	0.88[ASN][1000 genomes]
rs1968011	0.92[ASN][1000 genomes]
rs4975672	0.90[ASN][1000 genomes]
rs4975674	0.92[ASN][1000 genomes]
rs4975675	0.91[ASN][1000 genomes]
rs4975678	0.88[ASN][1000 genomes]
rs4975679	0.88[ASN][1000 genomes]
rs4975681	0.84[ASN][1000 genomes]
rs62335918	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6881649	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription 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 miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv880740	chr5:1468287-1671200	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
3	nsv881554	chr5:1468287-1696932	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
4	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
5	nsv881096	chr5:1503610-1671200	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
6	nsv10657	chr5:1544428-1633373	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv964815	chr5:1608931-1639317	Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv880390	chr5:1612612-1653418	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	esv3470307	chr5:1627006-1628941	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
10	esv3527255	chr5:1627027-1628889	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
11	esv3527256	chr5:1627045-1628940	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
12	esv3470306	chr5:1627062-1628907	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
13	esv3470309	chr5:1627140-1628842	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
14	esv3527257	chr5:1627140-1628842	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2354149	LOC728613///PDCD6	Cis_1M	lymphoblastoid	RTeQTL
rs2354149	LOC728613	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1595000-1634000	Weak transcription	Stomach Mucosa	stomach
2	chr5:1595200-1632800	Weak transcription	Brain Angular Gyrus	brain
3	chr5:1595200-1632800	Weak transcription	Right Ventricle	heart
4	chr5:1595400-1633200	Weak transcription	Primary B cells from cord blood	blood
5	chr5:1595400-1633200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:1595400-1633200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:1595400-1633200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:1597600-1632600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:1597600-1632800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:1597600-1632800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:1597600-1633000	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:1601400-1632800	Weak transcription	Hela-S3	cervix
13	chr5:1606200-1633200	Weak transcription	Brain Anterior Caudate	brain
14	chr5:1608800-1632800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:1608800-1633800	Weak transcription	Fetal Lung	lung
16	chr5:1609200-1633200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr5:1609200-1633200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:1609600-1633600	Weak transcription	Left Ventricle	heart
19	chr5:1610000-1633400	Weak transcription	Colonic Mucosa	Colon
20	chr5:1610600-1632800	Weak transcription	NHEK	skin
21	chr5:1610600-1633200	Weak transcription	Colon Smooth Muscle	Colon
22	chr5:1611800-1633800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:1613200-1633200	Weak transcription	HSMMtube	muscle
24	chr5:1613800-1633800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr5:1617000-1633200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr5:1617400-1632600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr5:1617400-1633200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:1619000-1633200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:1619400-1632800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr5:1619400-1633800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr5:1619600-1632400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr5:1619600-1632800	Weak transcription	GM12878-XiMat	blood
33	chr5:1619600-1633000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:1619600-1633800	Weak transcription	Placenta	Placenta
35	chr5:1620000-1629000	Weak transcription	Fetal Intestine Large	intestine
36	chr5:1620000-1630400	Weak transcription	Fetal Brain Female	brain
37	chr5:1620000-1633800	Weak transcription	Lung	lung
38	chr5:1620200-1629400	Weak transcription	Gastric	stomach
39	chr5:1620400-1633800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr5:1621600-1629000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:1621600-1633200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr5:1621600-1633200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr5:1621800-1632800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr5:1622000-1633200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr5:1622200-1633800	Weak transcription	Fetal Kidney	kidney
46	chr5:1622600-1632800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:1623200-1633200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr5:1623400-1633800	Weak transcription	Primary T cells from cord blood	blood
49	chr5:1624200-1633200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr5:1624400-1632800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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