Variant report

Variant	rs2624832
Chromosome Location	chr3:50030858-50030859
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50029898..50031827-chr3:50035708..50038441,2	K562	blood:

Variant related genes	Relation type
ENSG00000004534	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11130222	0.84[ASN][1000 genomes]
rs11706185	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11709503	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11709573	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11712056	0.83[ASN][1000 genomes]
rs11714324	0.88[ASN][1000 genomes]
rs11721204	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12107768	0.85[ASN][1000 genomes]
rs12634780	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13077403	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13079006	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13082703	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657664	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657688	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240328	0.82[ASN][1000 genomes]
rs2247510	0.81[ASN][1000 genomes]
rs2352969	0.95[ASN][1000 genomes]
rs2352984	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526747	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526749	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2526750	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2624815	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2624817	0.82[ASN][1000 genomes]
rs2624819	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2624821	0.98[ASN][1000 genomes]
rs2624822	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2624834	0.82[ASN][1000 genomes]
rs2681776	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681778	0.80[ASN][1000 genomes]
rs2681779	0.88[ASN][1000 genomes]
rs2883059	0.84[ASN][1000 genomes]
rs34034116	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34312088	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34654589	0.85[ASN][1000 genomes]
rs35012435	0.84[AFR][1000 genomes]
rs35275715	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36022378	0.81[ASN][1000 genomes]
rs3733134	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3774734	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3774759	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3796386	0.84[ASN][1000 genomes]
rs4688688	0.95[ASN][1000 genomes]
rs4688753	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4688754	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55692411	0.85[ASN][1000 genomes]
rs62262114	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62262118	0.80[AFR][1000 genomes]
rs6446191	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6446192	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6446194	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6446195	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6446197	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6762477	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6774354	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6793528	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6799579	0.85[ASN][1000 genomes]
rs7061	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7430334	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7613360	0.83[ASN][1000 genomes]
rs7615206	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7626952	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7627864	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7627910	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7634441	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7648174	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs868891	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs952594	0.85[ASN][1000 genomes]
rs9682295	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9812936	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9844201	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic 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	22 gene(s)	inside rSNPs	diseases
3	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	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
5	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2624832	RBM6	cis	Esophagus Mucosa	GTEx
rs2624832	RBM6	cis	Heart Left Ventricle	GTEx
rs2624832	RBM6	cis	Esophagus Muscularis	GTEx
rs2624832	RBM6	cis	lung	GTEx
rs2624832	RBM6	cis	Artery Aorta	GTEx
rs2624832	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2624832	RBM6	cis	Thyroid	GTEx
rs2624832	RBM6	cis	Adipose Subcutaneous	GTEx
rs2624832	RBM6	cis	Nerve Tibial	GTEx
rs2624832	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs2624832	RBM6	cis	Whole Blood	GTEx
rs2624832	RBM6	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49978800-50041000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:49992200-50037000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:49995400-50033200	Weak transcription	Fetal Brain Male	brain
4	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:49998400-50078600	Weak transcription	K562	blood
6	chr3:50002200-50057000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:50003000-50033400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:50004400-50044200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:50005000-50031400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:50005000-50036800	Weak transcription	Small Intestine	intestine
11	chr3:50005200-50033400	Weak transcription	Esophagus	oesophagus
12	chr3:50005200-50046400	Weak transcription	Psoas Muscle	Psoas
13	chr3:50005200-50050600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:50005400-50036800	Weak transcription	Brain Anterior Caudate	brain
15	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
16	chr3:50006200-50040800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:50008600-50050400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:50010800-50087000	Weak transcription	NHLF	lung
19	chr3:50011000-50031800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:50011000-50036600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr3:50011000-50036800	Weak transcription	Brain Angular Gyrus	brain
22	chr3:50011000-50037000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:50011000-50041000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:50011000-50046400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:50011000-50046400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:50011000-50048400	Weak transcription	A549	lung
27	chr3:50011000-50051000	Weak transcription	Pancreas	Pancrea
28	chr3:50011000-50078400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon
30	chr3:50011400-50035800	Weak transcription	Lung	lung
31	chr3:50012400-50049000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr3:50014800-50035800	Weak transcription	NHDF-Ad	bronchial
33	chr3:50015200-50031800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:50015200-50092000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:50015400-50046400	Weak transcription	Fetal Kidney	kidney
36	chr3:50015800-50033400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:50015800-50041000	Weak transcription	HSMMtube	muscle
38	chr3:50016000-50040800	Weak transcription	Brain Substantia Nigra	brain
39	chr3:50016600-50036800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:50016800-50037200	Weak transcription	Hela-S3	cervix
41	chr3:50017800-50035800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:50018800-50043600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:50021000-50031800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:50022200-50046400	Weak transcription	Gastric	stomach
45	chr3:50022600-50031600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:50022600-50033400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:50022600-50041200	Weak transcription	Aorta	Aorta
48	chr3:50022800-50031400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:50022800-50036600	Weak transcription	Spleen	Spleen
50	chr3:50023000-50035800	Weak transcription	NH-A	brain

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