Variant report

Variant	rs17328863
Chromosome Location	chr5:9543031-9543032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr5:9542726-9543064	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr5:9542366-9543907	IMR90	lung:	n/a	n/a
3	ELK1	chr5:9543007-9543035	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SNHG18	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11951006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11951779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11958229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1334	0.84[CEU][hapmap]
rs1508798	0.84[CEU][hapmap]
rs1651285	0.84[CEU][hapmap]
rs17262778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17263150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17263917	0.89[CEU][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17264034	0.80[EUR][1000 genomes]
rs17328408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17328904	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17328932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs374218	0.83[CEU][hapmap]
rs414829	0.88[CEU][hapmap]
rs431288	0.84[CEU][hapmap]
rs55891419	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55970326	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56411742	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs605126	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats 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
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv869120	chr5:9491731-10149255	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv1018275	chr5:9504897-9560199	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription 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	5 gene(s)	inside rSNPs	diseases
18	nsv537644	chr5:9504897-9560199	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv597073	chr5:9533854-9550642	Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	esv1824536	chr5:9539540-9546237	Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
21	esv1817081	chr5:9539540-9546451	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv597074	chr5:9541866-9546412	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv597075	chr5:9542529-9546412	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
24	esv1803881	chr5:9542529-9546451	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	nsv597076	chr5:9542529-9546451	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17328863	CTD-2001E22.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9521200-9544400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:9528400-9544200	Weak transcription	Fetal Intestine Small	intestine
3	chr5:9529600-9544400	Weak transcription	Pancreas	Pancrea
4	chr5:9529600-9544800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:9530200-9543600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr5:9530200-9544600	Weak transcription	Lung	lung
7	chr5:9530400-9544200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:9530400-9544800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:9533400-9543600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:9534200-9543200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:9535800-9544000	Weak transcription	Fetal Stomach	stomach
12	chr5:9536200-9543200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:9537400-9544200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:9538000-9544400	Weak transcription	Liver	Liver
15	chr5:9538600-9544400	Weak transcription	Left Ventricle	heart
16	chr5:9539400-9544400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:9541000-9543200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:9541000-9543200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:9541000-9543200	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr5:9541000-9543200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr5:9541000-9543200	Weak transcription	Right Atrium	heart
22	chr5:9541000-9544400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:9541400-9543200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:9541400-9543200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:9541800-9543200	Weak transcription	Osteobl	bone
26	chr5:9541800-9543800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:9542000-9543200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:9542200-9543200	Enhancers	Brain Anterior Caudate	brain
29	chr5:9542600-9543800	Flanking Active TSS	Fetal Heart	heart
30	chr5:9542800-9543200	Enhancers	Brain Angular Gyrus	brain
31	chr5:9542800-9543200	Enhancers	Brain Cingulate Gyrus	brain
32	chr5:9542800-9543200	Enhancers	Fetal Kidney	kidney
33	chr5:9542800-9543200	Enhancers	HMEC	breast
34	chr5:9542800-9543400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr5:9542800-9543400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:9542800-9544200	Enhancers	Brain Substantia Nigra	brain
37	chr5:9542800-9547200	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr5:9542800-9548400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:9543000-9543200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:9543000-9543200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:9543000-9543200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:9543000-9543200	Enhancers	NH-A	brain
43	chr5:9543000-9543400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
44	chr5:9543000-9543400	Flanking Active TSS	NHLF	lung
45	chr5:9543000-9543600	Enhancers	Fetal Lung	lung
46	chr5:9543000-9543800	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr5:9543000-9544000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:9543000-9544000	Enhancers	Muscle Satellite Cultured Cells	--
49	chr5:9543000-9544200	Flanking Active TSS	NHDF-Ad	bronchial
50	chr5:9543000-9544600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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