Variant report

Variant	rs9837341
Chromosome Location	chr3:49664767-49664768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49664437..49667415-chr3:49710388..49712286,2	K562	blood:
2	chr3:49663002..49665854-chr3:49667591..49669452,2	K562	blood:
3	chr3:49663253..49665357-chr3:49680487..49682256,2	K562	blood:
4	chr3:49664354..49666202-chr3:49667591..49669147,2	K562	blood:

Variant related genes	Relation type
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1050088	0.86[JPT][hapmap]
rs10865955	0.86[JPT][hapmap]
rs11130192	1.00[JPT][hapmap]
rs11130199	0.86[JPT][hapmap]
rs11130212	0.92[ASN][1000 genomes]
rs11130213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1131095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11709525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11710037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11711485	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs11718165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11720264	0.88[JPT][hapmap]
rs11720597	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11917431	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919311	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11921590	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489092	0.88[JPT][hapmap]
rs13064576	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13085791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13316695	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1352890	0.97[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];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873626	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2172252	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]
rs2329020	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2960548	0.82[ASN][1000 genomes]
rs3197999	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34762726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35007338	0.87[ASN][1000 genomes]
rs35404120	0.87[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];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4625	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs4855839	0.86[JPT][hapmap]
rs4855847	0.87[ASN][1000 genomes]
rs4855852	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4855859	0.86[JPT][hapmap]
rs4855864	0.86[JPT][hapmap]
rs4855881	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4855884	1.00[CHB][hapmap]
rs6766131	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs6770670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6803222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614725	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
rs7646366	1.00[CEU][hapmap];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];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9822268	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9823546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9824092	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833611	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836291	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9837027	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9837520	0.89[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];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9862080	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9875617	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9882740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9837341	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9837341	FAM212A	cis	Muscle Skeletal	GTEx
rs9837341	IHPK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49654400-49668200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:49655000-49668800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:49655600-49676200	Weak transcription	HepG2	liver
4	chr3:49657600-49685400	Weak transcription	Brain Substantia Nigra	brain
5	chr3:49660800-49682600	Weak transcription	Liver	Liver
6	chr3:49661000-49669200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:49661600-49692400	Weak transcription	Ovary	ovary
8	chr3:49661800-49682200	Weak transcription	Fetal Brain Male	brain
9	chr3:49662000-49667600	Strong transcription	Brain Germinal Matrix	brain
10	chr3:49662200-49666800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:49662400-49665800	Strong transcription	Fetal Brain Female	brain
12	chr3:49662600-49665200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:49662600-49668600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:49662800-49668400	Weak transcription	Lung	lung
15	chr3:49662800-49685000	Weak transcription	Right Ventricle	heart
16	chr3:49663000-49665000	Weak transcription	Fetal Stomach	stomach
17	chr3:49663600-49665400	Weak transcription	Brain Angular Gyrus	brain
18	chr3:49663600-49667000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:49663800-49679600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:49664000-49665000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:49664200-49668200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:49664200-49669000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:49664200-49683200	Weak transcription	Pancreas	Pancrea
24	chr3:49664400-49665200	Enhancers	Brain Anterior Caudate	brain
25	chr3:49664400-49668200	Weak transcription	NH-A	brain
26	chr3:49664600-49667800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:49664600-49674000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:49664600-49680000	Weak transcription	Brain Hippocampus Middle	brain

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