Variant report

Variant	rs3803009
Chromosome Location	chr12:26147707-26147708
allele	A/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	TCF12	chr12:26146925-26148004	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr12:26146985-26147777	SK-N-SH	brain:	n/a	n/a
3	JUND	chr12:26147032-26147786	SK-N-SH	brain:	n/a	chr12:26147692-26147701
4	NFIC	chr12:26147103-26147735	SK-N-SH	brain:	n/a	n/a
5	EP300	chr12:26146996-26147803	SK-N-SH	brain:	n/a	chr12:26147725-26147734
6	MEF2A	chr12:26146925-26147780	SK-N-SH	brain:	n/a	chr12:26147262-26147278 chr12:26147166-26147187 chr12:26147263-26147279 chr12:26147259-26147280 chr12:26147259-26147280 chr12:26147265-26147276 chr12:26147266-26147275 chr12:26147263-26147278
7	MEF2A	chr12:26147045-26147738	SK-N-SH	brain:	n/a	chr12:26147262-26147278 chr12:26147166-26147187 chr12:26147263-26147279 chr12:26147259-26147280 chr12:26147259-26147280 chr12:26147265-26147276 chr12:26147266-26147275 chr12:26147263-26147278
8	NFIC	chr12:26146986-26147959	SK-N-SH	brain:	n/a	n/a
9	TEAD4	chr12:26147012-26147726	SK-N-SH	brain:	n/a	n/a
10	EP300	chr12:26146972-26147771	SK-N-SH	brain:	n/a	chr12:26147725-26147734
11	PBX3	chr12:26147007-26147751	SK-N-SH	brain:	n/a	chr12:26147691-26147700
12	GATA3	chr12:26147016-26147896	SK-N-SH	brain:	n/a	n/a
13	FOSL2	chr12:26147151-26147712	SK-N-SH	brain:	n/a	chr12:26147692-26147701
14	TCF12	chr12:26146906-26147858	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
RASSF8	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10505990	0.81[JPT][hapmap]
rs10842643	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10842644	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10842653	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11048360	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11048372	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11048378	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11048379	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11048380	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11048381	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11048382	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11048383	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11048384	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11048389	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11048390	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1120064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1149804	0.88[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11561207	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12227689	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12578169	0.81[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes]
rs12579489	0.82[AMR][1000 genomes]
rs12581361	0.81[AMR][1000 genomes]
rs12812200	0.81[CHB][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12812752	0.94[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12813641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12818478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12831248	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1390326	0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes]
rs1495660	0.90[MEX][hapmap];0.82[AMR][1000 genomes]
rs1691889	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16929784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16929817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16929830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16929846	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16929940	0.81[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes]
rs16929945	0.81[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes]
rs16929950	0.81[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes]
rs16929958	0.81[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes]
rs16929973	0.84[CHD][hapmap];0.81[MEX][hapmap]
rs2055180	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2132317	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271481	0.80[CHD][hapmap];0.90[MEX][hapmap]
rs2279680	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2343201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2643941	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34294573	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34595529	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35924984	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3741546	0.84[CHD][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes]
rs3741547	0.81[AMR][1000 genomes]
rs58299475	0.82[AMR][1000 genomes]
rs59757232	0.82[AMR][1000 genomes]
rs60335536	0.84[AMR][1000 genomes]
rs61622173	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6487525	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs706524	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs706526	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs706531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs706532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs706533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs706538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7132590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7134721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7298162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7309394	0.86[CHD][hapmap];0.85[MEX][hapmap]
rs7953171	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7963603	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7963856	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs829837	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829987	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs853656	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758300	chr12:25992331-26161116	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	esv2759886	chr12:25992331-26161116	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS 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	38 gene(s)	inside rSNPs	diseases
3	nsv898931	chr12:26123345-26192936	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv522351	chr12:26127230-26149703	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26117600-26150000	Weak transcription	Hela-S3	cervix
2	chr12:26134200-26148000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:26134400-26147800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:26139400-26150600	Weak transcription	Brain Angular Gyrus	brain
5	chr12:26139600-26160000	Weak transcription	Pancreas	Pancrea
6	chr12:26142000-26149000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:26142200-26155600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:26143800-26151200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr12:26143800-26151200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr12:26144000-26151200	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr12:26144000-26151600	Enhancers	Colon Smooth Muscle	Colon
12	chr12:26144400-26148000	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr12:26144400-26148200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:26144400-26152200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr12:26144600-26148000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:26145000-26151400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr12:26145200-26148200	Enhancers	Fetal Lung	lung
18	chr12:26145200-26149600	Enhancers	H1 Cell Line	embryonic stem cell
19	chr12:26145200-26151200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:26145200-26151400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr12:26145200-26152600	Enhancers	Osteobl	bone
22	chr12:26145400-26148200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:26145400-26150400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr12:26145400-26150400	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr12:26145400-26150600	Weak transcription	Fetal Heart	heart
26	chr12:26145400-26151000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:26145600-26147800	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr12:26145600-26151800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:26145600-26163000	Weak transcription	Fetal Muscle Leg	muscle
30	chr12:26145800-26148400	Enhancers	Brain Substantia Nigra	brain
31	chr12:26145800-26150200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:26145800-26150600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:26145800-26152400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:26145800-26153400	Weak transcription	Right Atrium	heart
35	chr12:26146000-26150200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:26146000-26150200	Weak transcription	NHEK	skin
37	chr12:26146200-26148000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr12:26146200-26148200	Enhancers	Psoas Muscle	Psoas
39	chr12:26146200-26151200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:26146200-26152200	Enhancers	HSMM	muscle
41	chr12:26146200-26163000	Weak transcription	Lung	lung
42	chr12:26146400-26147800	Enhancers	Brain Hippocampus Middle	brain
43	chr12:26146400-26148200	Enhancers	Brain Cingulate Gyrus	brain
44	chr12:26146400-26148200	Enhancers	Fetal Stomach	stomach
45	chr12:26146400-26149200	Enhancers	Stomach Smooth Muscle	stomach
46	chr12:26146600-26148000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:26146600-26150200	Weak transcription	HMEC	breast
48	chr12:26146600-26150600	Weak transcription	Right Ventricle	heart
49	chr12:26146600-26155600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:26146800-26148000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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