Variant report

Variant	rs1968011
Chromosome Location	chr5:1624351-1624352
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11747600	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12658097	0.91[ASN][1000 genomes]
rs12658927	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13158448	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13176645	0.83[EUR][1000 genomes]
rs13181671	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2354149	0.92[ASN][1000 genomes]
rs4975561	0.87[EUR][1000 genomes]
rs4975672	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975674	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975675	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4975678	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4975679	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4975681	1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs62335918	0.83[ASN][1000 genomes]
rs6881649	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7700984	0.81[EUR][1000 genomes];0.86[ASN][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	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	nsv596879	chr5:1519079-1624351	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Enhancers 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	29 gene(s)	inside rSNPs	diseases
7	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
8	nsv596885	chr5:1552255-1624351	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	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
10	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
11	esv20103	chr5:1620571-1624351	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1968011	LOC728613///PDCD6	Cis_1M	lymphoblastoid	RTeQTL
rs1968011	PDCD6	cis	lesional skin	skin_eQTL
rs1968011	PDCD6///LOC650280///LOC653378	cis	lesional skin	skin_eQTL
rs1968011	LOC728613	Cis_1M	lymphoblastoid	RTeQTL
rs1968011	PDCD6	cis	uninvolved skin	skin_eQTL
rs1968011	PDCD6///LOC650280///LOC653378	cis	uninvolved skin	skin_eQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1595000-1626600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:1595000-1634000	Weak transcription	Stomach Mucosa	stomach
3	chr5:1595200-1632800	Weak transcription	Brain Angular Gyrus	brain
4	chr5:1595200-1632800	Weak transcription	Right Ventricle	heart
5	chr5:1595400-1633200	Weak transcription	Primary B cells from cord blood	blood
6	chr5:1595400-1633200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:1595400-1633200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:1595400-1633200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:1597600-1626400	Weak transcription	Adipose Nuclei	Adipose
10	chr5:1597600-1632600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:1597600-1632800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr5:1597600-1632800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:1597600-1633000	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:1601400-1632800	Weak transcription	Hela-S3	cervix
15	chr5:1606200-1633200	Weak transcription	Brain Anterior Caudate	brain
16	chr5:1607600-1626600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr5:1608400-1626400	Weak transcription	Pancreas	Pancrea
18	chr5:1608800-1624600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:1608800-1632800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:1608800-1633800	Weak transcription	Fetal Lung	lung
21	chr5:1609200-1633200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr5:1609200-1633200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr5:1609600-1633600	Weak transcription	Left Ventricle	heart
24	chr5:1609800-1626400	Weak transcription	HepG2	liver
25	chr5:1610000-1624400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:1610000-1633400	Weak transcription	Colonic Mucosa	Colon
27	chr5:1610600-1632800	Weak transcription	NHEK	skin
28	chr5:1610600-1633200	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:1611800-1633800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr5:1612200-1624400	Weak transcription	Aorta	Aorta
31	chr5:1613200-1633200	Weak transcription	HSMMtube	muscle
32	chr5:1613800-1633800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:1617000-1633200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr5:1617400-1632600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr5:1617400-1633200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:1619000-1633200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:1619200-1626400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr5:1619400-1632800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:1619400-1633800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr5:1619600-1626800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr5:1619600-1632400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr5:1619600-1632800	Weak transcription	GM12878-XiMat	blood
43	chr5:1619600-1633000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:1619600-1633800	Weak transcription	Placenta	Placenta
45	chr5:1620000-1629000	Weak transcription	Fetal Intestine Large	intestine
46	chr5:1620000-1630400	Weak transcription	Fetal Brain Female	brain
47	chr5:1620000-1633800	Weak transcription	Lung	lung
48	chr5:1620200-1629400	Weak transcription	Gastric	stomach
49	chr5:1620400-1633800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr5:1621000-1624800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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