Variant report

Variant	rs4927680
Chromosome Location	chr3:195659169-195659170
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	FOXA1	chr3:195659070-195659616	T-47D	breast:	n/a	n/a
2	POLR2A	chr3:195659045-195659312	MCF10A-Er-Src	breast:	n/a	n/a
3	FOXA1	chr3:195659111-195659608	T-47D	breast:	n/a	n/a
4	POLR2A	chr3:195659022-195659277	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RNU2-11P	TF binding region
ENSG00000231443	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12636596	0.86[AFR][1000 genomes]
rs6764284	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer 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 miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv1001387	chr3:195186128-195661538	Bivalent Enhancer Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
3	nsv428102	chr3:195201080-195829426	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv428430	chr3:195201080-195829426	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
6	nsv1006165	chr3:195383130-195777211	Bivalent Enhancer Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
7	nsv471621	chr3:195417664-195795474	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	esv2756651	chr3:195433543-195696720	Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
9	nsv432528	chr3:195433543-195696720	Enhancers Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
10	esv2754016	chr3:195433543-195753766	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Enhancers 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 miRNA	32 gene(s)	inside rSNPs	diseases
11	nsv822410	chr3:195438740-195725565	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
12	nsv1005193	chr3:195526571-195709662	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
13	nsv530397	chr3:195565159-195740416	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
14	nsv1002629	chr3:195582468-195769275	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
15	nsv1014602	chr3:195606770-195661538	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
16	nsv829827	chr3:195608866-195760829	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
17	nsv469518	chr3:195623722-195795474	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
18	nsv482784	chr3:195623722-195795474	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
19	nsv1010395	chr3:195641908-195848264	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
20	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
21	nsv967107	chr3:195648362-195697515	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
22	nsv10385	chr3:195650964-195739806	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
23	esv1822059	chr3:195651349-195776737	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
24	esv1844691	chr3:195651349-195776737	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
25	esv1820982	chr3:195651349-195835519	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
26	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4927680	AC024937.4	cis	Muscle Skeletal	GTEx
rs4927680	MUC20	cis	brain	BrainEAC
rs4927680	MUC4	cis	Nerve Tibial	GTEx
rs4927680	MUC20	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195647200-195681200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr3:195648600-195660400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:195648600-195666600	Weak transcription	Lung	lung
4	chr3:195648600-195666600	Weak transcription	Spleen	Spleen
5	chr3:195648600-195680600	Weak transcription	Pancreas	Pancrea
6	chr3:195648800-195666600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:195648800-195666800	Weak transcription	Esophagus	oesophagus
8	chr3:195649800-195659200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:195651200-195671200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:195651800-195673800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:195653000-195666800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:195655600-195660200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:195656600-195681000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:195656800-195666600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:195656800-195666600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:195656800-195669200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:195656800-195671200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:195656800-195676400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:195656800-195679400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:195657000-195659600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:195657000-195666800	Weak transcription	Primary T cells from cord blood	blood
22	chr3:195657200-195666800	Weak transcription	Thymus	Thymus
23	chr3:195657400-195670000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:195657800-195681400	Weak transcription	GM12878-XiMat	blood
25	chr3:195658200-195659600	Enhancers	Brain Anterior Caudate	brain
26	chr3:195658200-195660000	Enhancers	Brain Cingulate Gyrus	brain
27	chr3:195658200-195660000	Enhancers	Brain Substantia Nigra	brain
28	chr3:195658400-195659600	Enhancers	Brain Angular Gyrus	brain
29	chr3:195658400-195659800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:195658400-195660000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:195658400-195666800	Weak transcription	Gastric	stomach
32	chr3:195658600-195660000	Enhancers	Fetal Intestine Large	intestine
33	chr3:195658800-195659600	Enhancers	Brain Hippocampus Middle	brain
34	chr3:195658800-195660000	Enhancers	Fetal Muscle Trunk	muscle
35	chr3:195658800-195660000	Enhancers	Fetal Muscle Leg	muscle
36	chr3:195658800-195660600	Genic enhancers	Fetal Intestine Small	intestine
37	chr3:195658800-195666800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:195659000-195659600	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr3:195659000-195660600	Enhancers	HepG2	liver
40	chr3:195659000-195667200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:195659000-195676400	Weak transcription	Hela-S3	cervix

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