Variant report

Variant	rs1651283
Chromosome Location	chr5:9547129-9547130
allele	A/G
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	POLR2A	chr5:9544189-9548175	IMR90	lung:	n/a	n/a
2	MAZ	chr5:9544024-9548426	IMR90	lung:	n/a	chr5:9547821-9547831 chr5:9545804-9545814 chr5:9547149-9547159 chr5:9545538-9545548

No.	Distal block	Cell Line	Cell type
1	chr5:9546514..9548478-chr5:9550572..9552547,2	K562	blood:
2	chr5:9546585..9548880-chr5:9563821..9566752,2	K562	blood:
3	chr5:9546664..9548240-chr5:9561037..9563217,2	MCF-7	breast:

Variant related genes	Relation type
SEMA5A	TF binding region
SNORD123	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1334	1.00[JPT][hapmap]
rs1398337	0.80[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs1508798	1.00[JPT][hapmap]
rs1614229	0.84[JPT][hapmap]
rs1651284	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1651285	1.00[JPT][hapmap]
rs1706987	1.00[JPT][hapmap]
rs374218	1.00[JPT][hapmap]
rs414829	1.00[JPT][hapmap]
rs422309	1.00[JPT][hapmap]
rs422722	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs424773	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs431288	1.00[JPT][hapmap]
rs432989	1.00[JPT][hapmap]
rs456885	1.00[JPT][hapmap]
rs461337	1.00[JPT][hapmap]
rs461750	0.88[JPT][hapmap]
rs605126	1.00[JPT][hapmap]
rs788321	0.96[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	nsv1023329	chr5:9543307-9731720	Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
21	esv1817832	chr5:9545701-9547129	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	esv1839967	chr5:9545701-9547129	Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv597083	chr5:9546132-9547305	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1651283	SEMA5A	cis	cerebellum	SCAN
rs1651283	DAP	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9542800-9547200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr5:9542800-9548400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:9543000-9547200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:9543000-9547200	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr5:9543000-9547800	Active TSS	Brain Hippocampus Middle	brain
6	chr5:9543000-9548200	Active TSS	Aorta	Aorta
7	chr5:9543200-9547200	Active TSS	Brain Angular Gyrus	brain
8	chr5:9543200-9547400	Active TSS	Right Ventricle	heart
9	chr5:9543200-9548200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:9543200-9548200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr5:9543200-9548200	Active TSS	Right Atrium	heart
12	chr5:9543400-9548000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:9543400-9548400	Active TSS	NHLF	lung
14	chr5:9543600-9547200	Active TSS	Fetal Intestine Large	intestine
15	chr5:9543600-9548400	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr5:9543800-9547800	Active TSS	Fetal Lung	lung
17	chr5:9543800-9548000	Active TSS	Fetal Heart	heart
18	chr5:9543800-9548200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:9543800-9548200	Active TSS	Fetal Kidney	kidney
20	chr5:9543800-9548600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:9543800-9548800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:9543800-9548800	Active TSS	Placenta Amnion	Placenta Amnion
23	chr5:9544200-9547600	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr5:9544200-9548000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:9544200-9548000	Active TSS	Ovary	ovary
26	chr5:9544200-9548400	Active TSS	NHDF-Ad	bronchial
27	chr5:9544400-9547200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:9544400-9547200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:9544400-9547200	Active TSS	Left Ventricle	heart
30	chr5:9544400-9547400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:9544400-9547400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:9544400-9547400	Active TSS	Brain Cingulate Gyrus	brain
33	chr5:9544400-9547400	Active TSS	Brain Substantia Nigra	brain
34	chr5:9544400-9547600	Active TSS	Fetal Intestine Small	intestine
35	chr5:9544400-9547800	Active TSS	Pancreas	Pancrea
36	chr5:9544400-9548200	Active TSS	H9 Cell Line	embryonic stem cell
37	chr5:9544400-9548400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:9544400-9548400	Active TSS	Osteobl	bone
39	chr5:9544600-9547200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr5:9544600-9548000	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr5:9544600-9548400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:9544600-9548600	Active TSS	Muscle Satellite Cultured Cells	--
43	chr5:9545200-9547600	Active TSS	HSMM	muscle
44	chr5:9545200-9547800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:9545200-9548400	Active TSS	Duodenum Mucosa	Duodenum
46	chr5:9545400-9547200	Active TSS	Stomach Mucosa	stomach
47	chr5:9545400-9547800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr5:9545400-9548200	Active TSS	Brain Germinal Matrix	brain
49	chr5:9545600-9547200	Active TSS	Colon Smooth Muscle	Colon
50	chr5:9545600-9547800	Active TSS	HUES64 Cell Line	embryonic stem cell

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