Variant report

Variant	rs4677810
Chromosome Location	chr3:194856747-194856748
allele	C/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	MXI1	chr3:194854843-194857746	SK-N-SH	brain:	n/a	n/a
2	EP300	chr3:194855063-194857921	SK-N-SH	brain:	n/a	chr3:194856247-194856254
3	GATA2	chr3:194856570-194857194	SH-SY5Y	brain:	n/a	n/a
4	YY1	chr3:194856674-194857044	SK-N-SH_RA	brain:	n/a	n/a
5	GATA3	chr3:194856578-194857157	SH-SY5Y	brain:	n/a	n/a
6	REST	chr3:194856636-194857093	PFSK-1	brain:	n/a	chr3:194856958-194856967 chr3:194856960-194856967
7	POLR2A	chr3:194856617-194857041	H1-neurons	neurons:	n/a	n/a
8	EP300	chr3:194856652-194856989	SK-N-SH_RA	brain:	n/a	n/a
9	GATA3	chr3:194856652-194857161	SK-N-SH	brain:	n/a	n/a
10	RAD21	chr3:194856575-194857015	SK-N-SH_RA	brain:	n/a	n/a
11	YY1	chr3:194856672-194857008	SK-N-SH_RA	brain:	n/a	n/a
12	REST	chr3:194856650-194857018	SK-N-SH	brain:	n/a	chr3:194856958-194856967 chr3:194856960-194856967
13	GATA3	chr3:194856596-194857206	SK-N-SH	brain:	n/a	n/a
14	RCOR1	chr3:194856687-194856878	K562	blood:	n/a	n/a
15	POLR2A	chr3:194856621-194857006	H1-neurons	neurons:	n/a	n/a
16	EP300	chr3:194856651-194856968	SK-N-SH_RA	brain:	n/a	n/a
17	RAD21	chr3:194856671-194856998	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
MIR3137	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1009642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707930	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13314605	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1552893	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs2131876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172695	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs3892194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300953	0.86[CEU][hapmap]
rs4645095	0.81[AMR][1000 genomes]
rs4677663	0.81[CEU][hapmap]
rs4677812	0.87[CEU][hapmap]
rs4677813	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4677818	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55751800	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55879118	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6785310	0.90[JPT][hapmap]
rs750470	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7644208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874197	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs874198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs903310	0.81[CEU][hapmap]
rs950257	0.87[CEU][hapmap]
rs9848862	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv878137	chr3:194822098-194900432	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer 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
12	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
13	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
15	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194827400-194861200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:194831600-194857400	Weak transcription	Pancreas	Pancrea
3	chr3:194839200-194861200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:194839200-194861400	Weak transcription	Aorta	Aorta
5	chr3:194841000-194872800	Weak transcription	HSMMtube	muscle
6	chr3:194841400-194868800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:194844600-194860000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:194844800-194859800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:194845600-194858000	Weak transcription	Fetal Intestine Small	intestine
10	chr3:194845600-194861200	Weak transcription	Ovary	ovary
11	chr3:194846200-194862400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:194846600-194868400	Weak transcription	HepG2	liver
13	chr3:194847200-194868200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:194847600-194857800	Weak transcription	Spleen	Spleen
15	chr3:194847600-194858200	Weak transcription	Adipose Nuclei	Adipose
16	chr3:194849200-194861200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:194849400-194857000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:194849400-194858200	Weak transcription	Lung	lung
19	chr3:194850600-194859000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:194850800-194860400	Weak transcription	HUVEC	blood vessel
21	chr3:194850800-194860600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:194851600-194859800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:194851800-194860400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:194852000-194858000	Weak transcription	Placenta	Placenta
25	chr3:194852400-194868400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:194853000-194858000	Weak transcription	Fetal Thymus	thymus
27	chr3:194853000-194859600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:194854200-194858400	Weak transcription	Stomach Mucosa	stomach
29	chr3:194854600-194859600	Weak transcription	GM12878-XiMat	blood
30	chr3:194854600-194861600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:194854600-194865800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:194854600-194866200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:194854600-194868400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:194854600-194868600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:194854600-194871000	Weak transcription	Fetal Brain Female	brain
36	chr3:194854800-194858400	Weak transcription	NHEK	skin
37	chr3:194854800-194859800	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:194854800-194860400	Weak transcription	NH-A	brain
39	chr3:194854800-194860600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:194854800-194861200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:194854800-194868400	Weak transcription	NHLF	lung
42	chr3:194855200-194861600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:194855200-194862800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:194855400-194859800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:194855400-194860400	Weak transcription	Hela-S3	cervix
46	chr3:194855400-194868800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:194855600-194857600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:194855600-194859600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr3:194855600-194859600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:194856000-194856800	Enhancers	K562	blood

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