Variant report

Variant	rs11922013
Chromosome Location	chr3:49458355-49458356
allele	C/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	POLR2A	chr3:49456096-49460980	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49170472..49172068-chr3:49457076..49459891,2	MCF-7	breast:
2	chr3:49457686..49462880-chr3:49464384..49468098,7	MCF-7	breast:

Variant related genes	Relation type
AMT	TF binding region
NICN1-AS1	TF binding region
ENSG00000145029	Chromatin interaction
ENSG00000172037	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10212296	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1050088	1.00[JPT][hapmap]
rs1050450	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865955	1.00[JPT][hapmap]
rs11130192	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11130193	0.83[ASN][1000 genomes]
rs11130196	0.82[ASN][1000 genomes]
rs11130199	1.00[JPT][hapmap]
rs11706370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11711536	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11712569	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11713474	0.83[AMR][1000 genomes]
rs11715915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716974	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719996	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11720264	1.00[JPT][hapmap]
rs11919311	0.82[JPT][hapmap]
rs11926781	0.82[AMR][1000 genomes]
rs12330269	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12489092	1.00[JPT][hapmap]
rs13079082	0.88[AMR][1000 genomes]
rs13079643	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13086611	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13087851	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13090388	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1464566	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1464567	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1464568	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1568661	1.00[JPT][hapmap]
rs17080528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17650792	1.00[JPT][hapmap]
rs1800668	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1801143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs1987628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34196454	0.86[AMR][1000 genomes]
rs34293138	0.86[AMR][1000 genomes]
rs34363169	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34427167	0.82[AMR][1000 genomes]
rs34588335	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34937635	0.87[ASN][1000 genomes]
rs35115732	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35169793	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35261698	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35701831	1.00[JPT][hapmap]
rs35999162	0.80[AMR][1000 genomes]
rs3811697	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs3811699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3870338	1.00[JPT][hapmap]
rs3924462	1.00[JPT][hapmap]
rs3926569	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4459909	0.94[ASN][1000 genomes]
rs4625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs4855839	1.00[JPT][hapmap]
rs4855842	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4855843	0.83[ASN][1000 genomes]
rs4855852	0.82[JPT][hapmap]
rs4855859	1.00[JPT][hapmap]
rs4855864	1.00[JPT][hapmap]
rs4855873	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4855877	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs55957735	0.92[ASN][1000 genomes]
rs6446264	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6446272	0.91[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446274	0.87[ASN][1000 genomes]
rs6446277	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67216675	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67485053	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6766131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6766581	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6779524	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782577	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6784820	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6792911	0.86[ASN][1000 genomes]
rs6793308	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6797664	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6809216	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71324962	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7622302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7623659	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7630869	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7633271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7637999	1.00[JPT][hapmap]
rs7643586	0.86[ASN][1000 genomes]
rs7646366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7648841	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs885592	1.00[JPT][hapmap]
rs9811982	1.00[CEU][hapmap]
rs9814873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9818590	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9818758	1.00[CHB][hapmap]
rs9821311	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9827021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9827708	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs9837027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs9841110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9850072	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9853683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9858280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs9858418	0.88[AMR][1000 genomes]
rs9859556	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9871380	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873994	1.00[CHB][hapmap]
rs9875617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs9878943	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11922013	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs11922013	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs11922013	FAM212A	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49450400-49459000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49450400-49459400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49450600-49459000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:49450800-49459000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:49450800-49459200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:49450800-49459200	Genic enhancers	Placenta	Placenta
7	chr3:49451200-49459000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:49451200-49459400	Weak transcription	Fetal Brain Male	brain
9	chr3:49451200-49466200	Weak transcription	Psoas Muscle	Psoas
10	chr3:49451400-49459400	Weak transcription	Ovary	ovary
11	chr3:49452400-49458400	Strong transcription	Fetal Brain Female	brain
12	chr3:49453400-49458400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr3:49453600-49459000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:49453800-49459000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:49454000-49459400	Weak transcription	Brain Angular Gyrus	brain
16	chr3:49454400-49458600	Weak transcription	HUVEC	blood vessel
17	chr3:49454600-49458800	Strong transcription	Fetal Stomach	stomach
18	chr3:49454800-49458800	Weak transcription	Stomach Mucosa	stomach
19	chr3:49454800-49459000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:49454800-49459000	Strong transcription	Thymus	Thymus
21	chr3:49454800-49459200	Weak transcription	Fetal Kidney	kidney
22	chr3:49455000-49459000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:49455000-49459000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:49455200-49458800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:49455200-49459000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:49455200-49459400	Weak transcription	Brain Germinal Matrix	brain
27	chr3:49455200-49459400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:49455200-49459600	Enhancers	Hela-S3	cervix
29	chr3:49455400-49458400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:49455400-49459000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:49455400-49459000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:49455400-49459000	Weak transcription	Colonic Mucosa	Colon
33	chr3:49455400-49459000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:49455400-49461800	Weak transcription	Aorta	Aorta
35	chr3:49455600-49458600	Weak transcription	Right Ventricle	heart
36	chr3:49455600-49459000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:49455600-49459000	Strong transcription	Fetal Muscle Leg	muscle
38	chr3:49455600-49459000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:49455600-49459200	Weak transcription	Left Ventricle	heart
40	chr3:49455600-49459400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr3:49455600-49460000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:49455600-49461600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr3:49455600-49461800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:49455600-49466200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:49455800-49458400	Strong transcription	Fetal Thymus	thymus
46	chr3:49455800-49459200	Weak transcription	Brain Substantia Nigra	brain
47	chr3:49455800-49463800	Strong transcription	Dnd41	blood
48	chr3:49456200-49458400	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr3:49456400-49459600	Enhancers	Esophagus	oesophagus
50	chr3:49456600-49458400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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