Variant report

Variant	rs2172252
Chromosome Location	chr3:49678307-49678308
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49585320..49587935-chr3:49676099..49678339,2	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1050088	0.86[JPT][hapmap]
rs1060962	0.81[ASN][1000 genomes]
rs10865955	0.86[JPT][hapmap]
rs11130199	0.86[JPT][hapmap]
rs11130212	0.97[ASN][1000 genomes]
rs11130213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1131095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11709525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710037	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711485	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs11718165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11720264	0.88[JPT][hapmap]
rs11720597	0.85[AMR][1000 genomes]
rs11917431	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11919311	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11921590	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12489092	0.88[JPT][hapmap]
rs13064576	0.85[AMR][1000 genomes]
rs13085791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13316695	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352890	0.92[ASN][1000 genomes]
rs1568661	0.86[JPT][hapmap]
rs1801143	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs1873625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1873626	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2005557	0.81[ASN][1000 genomes]
rs2131104	0.81[ASN][1000 genomes]
rs2329020	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2960548	0.87[ASN][1000 genomes]
rs3197999	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34762726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35007338	0.92[ASN][1000 genomes]
rs35404120	0.92[ASN][1000 genomes]
rs35701831	0.86[JPT][hapmap]
rs3811697	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs3870338	0.86[JPT][hapmap]
rs3924462	0.86[JPT][hapmap]
rs4283605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs4855839	0.86[JPT][hapmap]
rs4855847	0.92[ASN][1000 genomes]
rs4855852	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4855859	0.86[JPT][hapmap]
rs4855864	0.86[JPT][hapmap]
rs4855881	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4855884	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6765869	0.81[ASN][1000 genomes]
rs6766131	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs6770670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7614725	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7622302	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs7633271	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs7637999	0.86[JPT][hapmap]
rs885592	0.86[JPT][hapmap]
rs9811982	1.00[CEU][hapmap]
rs9812791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822268	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9823546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9824092	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827021	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs9827708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9833611	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9836291	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9837027	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9837341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9837520	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9841110	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs9853683	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9858213	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs9858280	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9858542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862080	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875617	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes]
rs9882740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv3812	chr3:49669773-49680587	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2172252	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2172252	FAM212A	cis	Muscle Skeletal	GTEx
rs2172252	IHPK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49657600-49685400	Weak transcription	Brain Substantia Nigra	brain
2	chr3:49660800-49682600	Weak transcription	Liver	Liver
3	chr3:49661600-49692400	Weak transcription	Ovary	ovary
4	chr3:49661800-49682200	Weak transcription	Fetal Brain Male	brain
5	chr3:49662800-49685000	Weak transcription	Right Ventricle	heart
6	chr3:49663800-49679600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:49664200-49683200	Weak transcription	Pancreas	Pancrea
8	chr3:49664600-49680000	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:49667600-49679800	Weak transcription	Brain Germinal Matrix	brain
10	chr3:49669400-49692000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:49669600-49679400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:49669600-49679800	Weak transcription	Fetal Brain Female	brain
13	chr3:49669600-49680000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:49670000-49680000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:49673800-49692400	Weak transcription	Gastric	stomach
16	chr3:49674400-49680000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:49675000-49679400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:49675000-49680400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:49675400-49688200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:49675600-49679600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:49676000-49686400	Weak transcription	Spleen	Spleen
22	chr3:49676200-49679200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:49676200-49692000	Weak transcription	Esophagus	oesophagus
24	chr3:49676400-49678400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:49676400-49678600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:49676400-49679600	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:49676400-49679600	Weak transcription	HSMMtube	muscle
28	chr3:49676400-49687000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr3:49676600-49680400	Weak transcription	HepG2	liver
30	chr3:49677200-49679800	Weak transcription	Fetal Stomach	stomach
31	chr3:49677400-49680200	Weak transcription	Brain Anterior Caudate	brain
32	chr3:49677600-49680000	Weak transcription	Brain Angular Gyrus	brain
33	chr3:49678200-49678800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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