Variant report

Variant	rs4687587
Chromosome Location	chr3:53849510-53849511
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10510765	1.00[CHB][hapmap]
rs10510766	1.00[CHB][hapmap]
rs11705918	1.00[CHB][hapmap]
rs11706303	1.00[CHB][hapmap]
rs11708227	1.00[CHB][hapmap]
rs11709505	1.00[CHB][hapmap]
rs11719179	1.00[CHB][hapmap]
rs12676	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13062035	1.00[ASN][1000 genomes]
rs13076366	1.00[CHB][hapmap]
rs13076915	1.00[CHB][hapmap]
rs13082692	1.00[CHB][hapmap]
rs14165	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17053338	1.00[CHB][hapmap]
rs17641133	1.00[CHB][hapmap]
rs34565662	1.00[ASN][1000 genomes]
rs34723699	1.00[ASN][1000 genomes]
rs36006337	1.00[ASN][1000 genomes]
rs36077841	1.00[ASN][1000 genomes]
rs4687586	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62250900	1.00[ASN][1000 genomes]
rs6445606	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71301848	1.00[ASN][1000 genomes]
rs893362	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893363	1.00[CHB][hapmap]
rs920252	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836592	0.92[CEU][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1003204	chr3:53820070-53877149	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1002375	chr3:53822319-53872753	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv518466	chr3:53832903-53882663	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv521181	chr3:53833509-53881471	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4687587	CHDH	cis	parietal	SCAN
rs4687587	ACTR8	cis	parietal	SCAN
rs4687587	CHDH	cis	Nerve Tibial	GTEx
rs4687587	HEMK1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53829200-53853000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:53830400-53851200	Weak transcription	Fetal Brain Male	brain
3	chr3:53839000-53849800	Strong transcription	Fetal Lung	lung
4	chr3:53839200-53855200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:53839400-53851400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:53839600-53851000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:53839600-53851200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:53839600-53852800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:53839600-53876600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:53840600-53851200	Weak transcription	Aorta	Aorta
11	chr3:53840800-53853600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:53841000-53852600	Weak transcription	Ovary	ovary
13	chr3:53841000-53852800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:53841400-53850400	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:53841600-53851000	Weak transcription	Brain Angular Gyrus	brain
16	chr3:53841600-53851200	Weak transcription	Colonic Mucosa	Colon
17	chr3:53841600-53851400	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:53841600-53851400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:53841600-53855600	Weak transcription	Right Ventricle	heart
20	chr3:53841600-53855800	Weak transcription	Right Atrium	heart
21	chr3:53841800-53850600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:53841800-53850600	Weak transcription	HepG2	liver
23	chr3:53841800-53851200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:53841800-53853400	Weak transcription	Fetal Brain Female	brain
25	chr3:53841800-53853400	Weak transcription	GM12878-XiMat	blood
26	chr3:53842200-53852200	Strong transcription	Fetal Intestine Small	intestine
27	chr3:53842200-53852600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:53842200-53857200	Strong transcription	Fetal Intestine Large	intestine
29	chr3:53842400-53855600	Weak transcription	Fetal Heart	heart
30	chr3:53844400-53852000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:53844600-53851200	Weak transcription	Spleen	Spleen
32	chr3:53845400-53850800	Weak transcription	Gastric	stomach
33	chr3:53846200-53850800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:53846600-53879800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:53846800-53851200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:53847000-53856400	Weak transcription	Brain Germinal Matrix	brain
37	chr3:53847000-53862000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:53847600-53852200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:53848000-53849600	Strong transcription	Brain Anterior Caudate	brain
40	chr3:53848200-53850200	Weak transcription	Brain Substantia Nigra	brain
41	chr3:53848200-53851800	Weak transcription	Esophagus	oesophagus
42	chr3:53849000-53850000	Genic enhancers	Brain Cingulate Gyrus	brain
43	chr3:53849000-53850000	Strong transcription	Lung	lung
44	chr3:53849000-53857200	Strong transcription	Duodenum Mucosa	Duodenum
45	chr3:53849000-53857800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:53849000-53858200	Strong transcription	Fetal Stomach	stomach
47	chr3:53849000-53858800	Strong transcription	Liver	Liver
48	chr3:53849000-53859200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:53849000-53866800	Weak transcription	Stomach Mucosa	stomach
50	chr3:53849200-53849600	Strong transcription	Brain Inferior Temporal Lobe	brain

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