Variant report

Variant	rs2624824
Chromosome Location	chr3:50088266-50088267
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	JUND	chr3:50087699-50088340	SK-N-SH	brain:	n/a	chr3:50088005-50088016
2	TEAD4	chr3:50087876-50088396	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr3:50087292-50088376	SK-N-SH	brain:	n/a	n/a
4	FOSL2	chr3:50087644-50088328	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr3:50087722-50088313	SK-N-SH	brain:	n/a	n/a
6	EP300	chr3:50087664-50088380	SK-N-SH	brain:	n/a	n/a
7	JUND	chr3:50087587-50088333	SK-N-SH	brain:	n/a	chr3:50088005-50088016
8	EP300	chr3:50087724-50088380	SK-N-SH_RA	brain:	n/a	n/a
9	PBX3	chr3:50087369-50088301	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr3:50087233-50088404	SK-N-SH	brain:	n/a	n/a
11	TCF12	chr3:50087272-50088471	SK-N-SH	brain:	n/a	n/a
12	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: 80 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10049087	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1062633	0.85[CEU][hapmap]
rs11130226	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11130228	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11130233	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130234	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11713562	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11925192	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12485600	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12496973	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13060128	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2008877	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2013208	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071206	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2071207	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2230590	0.88[CEU][hapmap]
rs2240326	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240327	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240329	0.96[CEU][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2245365	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2252833	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2280406	0.88[CEU][hapmap]
rs2301166	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2353579	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2353586	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2353587	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2526743	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2526748	0.96[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526751	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2526754	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2624816	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2624823	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2624825	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2624843	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2624853	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2681780	0.92[CEU][hapmap]
rs2681781	0.92[CEU][hapmap]
rs2777888	0.92[CEU][hapmap]
rs2856234	0.96[CEU][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2856236	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2883057	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34080578	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34831713	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35065728	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3733133	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774733	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4688686	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4688689	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4688690	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4688755	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688756	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4688757	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4688758	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6446193	0.96[CEU][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66851636	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6765484	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6767381	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6771546	0.96[CEU][hapmap]
rs6772095	0.96[CEU][hapmap]
rs6780731	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6792892	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7428430	0.87[CEU][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7613875	0.82[CEU][hapmap]
rs7621026	0.96[CEU][hapmap]
rs7621352	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7628058	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7635002	0.81[EUR][1000 genomes]
rs7642934	0.89[EUR][1000 genomes]
rs7650214	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9311446	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9810125	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9814664	0.96[CEU][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9821675	0.89[CEU][hapmap]
rs9853222	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9856572	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9861216	0.96[CEU][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9866695	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2624824	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2624824	RBM6	cis	Adipose Subcutaneous	GTEx
rs2624824	RBM6	cis	Whole Blood	GTEx
rs2624824	RBM6	cis	Artery Aorta	GTEx
rs2624824	RBM6	cis	Thyroid	GTEx
rs2624824	RBM6	cis	Stomach	GTEx
rs2624824	RBM6	cis	Esophagus Muscularis	GTEx
rs2624824	RBM6	cis	Heart Left Ventricle	GTEx
rs2624824	RBM6	cis	Nerve Tibial	GTEx
rs2624824	RBM6	cis	Artery Tibial	GTEx
rs2624824	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs2624824	RBM6	cis	Esophagus Mucosa	GTEx
rs2624824	RBM6	cis	lung	GTEx

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	chr3:50084600-50104600	Strong transcription	Placenta	Placenta
42	chr3:50084600-50113400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:50084600-50114600	Strong transcription	Adipose Nuclei	Adipose
44	chr3:50084800-50113400	Strong transcription	Dnd41	blood
45	chr3:50085000-50092800	Strong transcription	Fetal Brain Female	brain
46	chr3:50085000-50113600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:50085000-50114800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr3:50085000-50115800	Strong transcription	Liver	Liver
49	chr3:50085200-50109200	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr3:50085200-50111600	Strong transcription	Primary neutrophils fromperipheralblood	blood

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