Variant report

Variant	rs62263580
Chromosome Location	chr3:50087725-50087726
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	GATA3	chr3:50087570-50088031	SH-SY5Y	brain:	n/a	n/a
2	JUND	chr3:50087699-50088340	SK-N-SH	brain:	n/a	chr3:50088005-50088016
3	GATA3	chr3:50087292-50088376	SK-N-SH	brain:	n/a	n/a
4	TEAD4	chr3:50087592-50088253	SK-N-SH	brain:	n/a	n/a
5	MAZ	chr3:50087674-50088215	IMR90	lung:	n/a	n/a
6	FOSL2	chr3:50087644-50088328	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr3:50087644-50088261	A549	lung:	n/a	n/a
8	POLR2A	chr3:50087722-50088313	SK-N-SH	brain:	n/a	n/a
9	EP300	chr3:50087664-50088380	SK-N-SH	brain:	n/a	n/a
10	JUND	chr3:50087587-50088333	SK-N-SH	brain:	n/a	chr3:50088005-50088016
11	EP300	chr3:50087724-50088380	SK-N-SH_RA	brain:	n/a	n/a
12	PBX3	chr3:50087369-50088301	SK-N-SH	brain:	n/a	n/a
13	GATA3	chr3:50087233-50088404	SK-N-SH	brain:	n/a	n/a
14	TCF12	chr3:50087272-50088471	SK-N-SH	brain:	n/a	n/a
15	PBX3	chr3:50087647-50088238	SK-N-SH	brain:	n/a	n/a
16	TCF12	chr3:50087456-50088546	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
RBM6	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs11130223	0.88[EUR][1000 genomes]
rs11130225	0.84[EUR][1000 genomes]
rs11130230	0.88[EUR][1000 genomes]
rs11130237	0.88[EUR][1000 genomes]
rs11130239	0.88[EUR][1000 genomes]
rs11130240	0.90[EUR][1000 genomes]
rs11916261	0.88[EUR][1000 genomes]
rs11916999	0.96[EUR][1000 genomes]
rs11920034	1.00[EUR][1000 genomes]
rs11923132	0.88[EUR][1000 genomes]
rs11924670	0.96[EUR][1000 genomes]
rs11924711	1.00[EUR][1000 genomes]
rs11925156	0.88[EUR][1000 genomes]
rs11928995	0.81[EUR][1000 genomes]
rs12486470	1.00[EUR][1000 genomes]
rs12486808	0.92[EUR][1000 genomes]
rs12486832	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12489386	0.88[EUR][1000 genomes]
rs12490944	0.92[EUR][1000 genomes]
rs12492291	0.96[EUR][1000 genomes]
rs12493565	0.92[EUR][1000 genomes]
rs12494077	0.96[EUR][1000 genomes]
rs12494172	0.96[EUR][1000 genomes]
rs12494916	0.96[EUR][1000 genomes]
rs12495114	1.00[EUR][1000 genomes]
rs12495831	0.88[EUR][1000 genomes]
rs12629129	0.92[EUR][1000 genomes]
rs12629553	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12629677	0.92[EUR][1000 genomes]
rs12630917	0.88[EUR][1000 genomes]
rs12630959	0.88[EUR][1000 genomes]
rs12631248	1.00[EUR][1000 genomes]
rs12631306	0.88[EUR][1000 genomes]
rs12631309	0.88[EUR][1000 genomes]
rs12631608	0.88[EUR][1000 genomes]
rs12632751	0.96[EUR][1000 genomes]
rs12636045	0.81[EUR][1000 genomes]
rs12636232	0.81[EUR][1000 genomes]
rs12636669	0.88[EUR][1000 genomes]
rs12637222	0.88[EUR][1000 genomes]
rs12637457	0.92[EUR][1000 genomes]
rs12637681	0.85[EUR][1000 genomes]
rs12638046	0.92[EUR][1000 genomes]
rs1317215	0.88[EUR][1000 genomes]
rs13326300	0.88[EUR][1000 genomes]
rs2023951	0.96[EUR][1000 genomes]
rs2023952	0.96[EUR][1000 genomes]
rs28478136	0.88[EUR][1000 genomes]
rs35333166	0.88[EUR][1000 genomes]
rs41291716	0.92[EUR][1000 genomes]
rs55643042	0.88[EUR][1000 genomes]
rs57009357	0.92[EUR][1000 genomes]
rs57575459	0.92[EUR][1000 genomes]
rs58025924	0.92[EUR][1000 genomes]
rs58621288	0.88[EUR][1000 genomes]
rs58766761	0.92[EUR][1000 genomes]
rs59802870	0.96[EUR][1000 genomes]
rs61491513	0.88[EUR][1000 genomes]
rs61729114	0.92[EUR][1000 genomes]
rs62260756	0.88[EUR][1000 genomes]
rs62260770	0.81[EUR][1000 genomes]
rs62260771	0.81[EUR][1000 genomes]
rs62262060	0.88[EUR][1000 genomes]
rs62262095	0.92[EUR][1000 genomes]
rs62262096	0.92[EUR][1000 genomes]
rs62262099	0.92[EUR][1000 genomes]
rs62262100	0.92[EUR][1000 genomes]
rs62262104	0.86[EUR][1000 genomes]
rs62262105	0.88[EUR][1000 genomes]
rs62262116	0.88[EUR][1000 genomes]
rs62262117	0.88[EUR][1000 genomes]
rs62262138	0.88[EUR][1000 genomes]
rs62262144	0.88[EUR][1000 genomes]
rs62262145	0.88[EUR][1000 genomes]
rs62262148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62263578	0.92[EUR][1000 genomes]
rs62263584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62263586	0.96[EUR][1000 genomes]
rs62263588	0.96[EUR][1000 genomes]
rs62263590	0.96[EUR][1000 genomes]
rs62263591	0.96[EUR][1000 genomes]
rs62263596	0.84[EUR][1000 genomes]
rs62263600	0.81[EUR][1000 genomes]
rs6797500	0.88[EUR][1000 genomes]
rs9813644	0.88[EUR][1000 genomes]
rs9859813	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon
2	chr3:50015200-50092000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:50041400-50095200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:50041600-50093400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:50047200-50092600	Weak transcription	Gastric	stomach
6	chr3:50051600-50095200	Weak transcription	Pancreas	Pancrea
7	chr3:50056400-50114400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:50062000-50091400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:50062200-50093400	Weak transcription	Small Intestine	intestine
10	chr3:50072800-50095200	Weak transcription	Fetal Heart	heart
11	chr3:50078400-50102400	Weak transcription	Psoas Muscle	Psoas
12	chr3:50078800-50092000	Weak transcription	Ovary	ovary
13	chr3:50079200-50095200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:50079200-50095200	Weak transcription	K562	blood
15	chr3:50081600-50089800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:50082000-50113600	Strong transcription	Primary T cells from cord blood	blood
17	chr3:50082000-50115600	Strong transcription	Fetal Intestine Large	intestine
18	chr3:50082200-50112000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr3:50082200-50116000	Strong transcription	Fetal Muscle Leg	muscle
20	chr3:50082400-50113400	Strong transcription	Primary B cells from cord blood	blood
21	chr3:50082400-50115800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr3:50082400-50116200	Strong transcription	Fetal Thymus	thymus
23	chr3:50082600-50116200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:50083400-50113200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:50083800-50098000	Strong transcription	Fetal Intestine Small	intestine
26	chr3:50083800-50111600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:50084000-50090200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:50084000-50093200	Strong transcription	Fetal Stomach	stomach
29	chr3:50084000-50105200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:50084000-50113400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:50084000-50114800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:50084000-50114800	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr3:50084200-50090400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:50084200-50092800	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:50084200-50095000	Weak transcription	Aorta	Aorta
36	chr3:50084200-50115000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:50084200-50116600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:50084400-50089800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:50084400-50112200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr3:50084400-50115800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:50084600-50088000	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:50084600-50088000	Strong transcription	GM12878-XiMat	blood
43	chr3:50084600-50088200	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr3:50084600-50104600	Strong transcription	Placenta	Placenta
45	chr3:50084600-50113400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:50084600-50114600	Strong transcription	Adipose Nuclei	Adipose
47	chr3:50084800-50113400	Strong transcription	Dnd41	blood
48	chr3:50085000-50087800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:50085000-50088200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:50085000-50092800	Strong transcription	Fetal Brain Female	brain

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