Variant report

Variant	rs11715915
Chromosome Location	chr3:49455330-49455331
allele	C/T
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	chr3:49455178-49455390	HCT-116	colon:	n/a	n/a
2	POLR2A	chr3:49455139-49455525	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:49454273-49455717	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr3:49452993-49456018	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:49454990-49455431	MCF-7	breast:	n/a	n/a
6	POLR2A	chr3:49454919-49455447	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr3:49455320-49455470	GM12864	blood:	n/a	n/a
8	POLR2A	chr3:49454881-49455343	MCF-7	breast:	n/a	n/a
9	POLR2A	chr3:49455006-49455467	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49453314..49456247-chr3:49456435..49459274,2	MCF-7	breast:
2	chr3:49449761..49451817-chr3:49454782..49457438,2	MCF-7	breast:

Variant related genes	Relation type
RHOA	TF binding region
ENSG00000145022	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000145020	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10212296	0.82[AMR][1000 genomes]
rs1050088	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1050450	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10640	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865955	0.93[CHD][hapmap];0.85[GIH][hapmap];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	0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs11706370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711485	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11711536	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11712569	0.85[AMR][1000 genomes]
rs11713474	0.82[AMR][1000 genomes]
rs11716974	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719996	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11720264	1.00[JPT][hapmap]
rs11922013	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]
rs11926781	0.83[AMR][1000 genomes]
rs12330269	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12489092	1.00[JPT][hapmap]
rs13078949	0.85[GIH][hapmap]
rs13079082	0.83[AMR][1000 genomes]
rs13079643	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13086611	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13087851	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13090388	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1464566	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1464567	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1464568	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1568661	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs17080528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17650792	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1800668	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1801143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes]
rs1987628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34196454	0.85[AMR][1000 genomes]
rs34293138	0.85[AMR][1000 genomes]
rs34363169	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34427167	0.83[AMR][1000 genomes]
rs34588335	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34937635	0.87[ASN][1000 genomes]
rs35115732	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35169793	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35261698	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35701831	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs35999162	0.82[AMR][1000 genomes]
rs3811697	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes]
rs3811699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3870338	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3924462	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3926569	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4459909	0.94[ASN][1000 genomes]
rs4625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes]
rs4855839	0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs4855842	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4855843	0.83[ASN][1000 genomes]
rs4855852	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs4855859	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855864	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855873	0.93[CHD][hapmap];0.85[GIH][hapmap];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	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6446272	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446274	0.87[ASN][1000 genomes]
rs6446277	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67216675	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67485053	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6766131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6766581	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6779524	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782577	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6784820	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6792911	0.86[ASN][1000 genomes]
rs6793308	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6797664	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6809216	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71324962	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7622302	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7623659	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7630869	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7633271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7637999	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7643586	0.86[ASN][1000 genomes]
rs7646366	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7648841	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs885592	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9811982	1.00[CEU][hapmap]
rs9814873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9818590	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9821311	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9827021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9827708	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap]
rs9837027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes]
rs9841110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9850072	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9853683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9858280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes]
rs9858418	0.83[AMR][1000 genomes]
rs9859556	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9871380	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875617	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap]
rs9878943	0.98[AMR][1000 genomes];0.99[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11715915	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs11715915	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs11715915	FAM212A	cis	Muscle Skeletal	GTEx
rs11715915	USP4	cis	multi-tissue	Pritchard

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	chr3:49450800-49455400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:49450800-49457800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:49450800-49459000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:49450800-49459200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:49450800-49459200	Genic enhancers	Placenta	Placenta
9	chr3:49451000-49458000	Weak transcription	Small Intestine	intestine
10	chr3:49451200-49459000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:49451200-49459400	Weak transcription	Fetal Brain Male	brain
12	chr3:49451200-49466200	Weak transcription	Psoas Muscle	Psoas
13	chr3:49451400-49459400	Weak transcription	Ovary	ovary
14	chr3:49451600-49458000	Strong transcription	NHLF	lung
15	chr3:49451600-49458200	Strong transcription	Fetal Intestine Small	intestine
16	chr3:49451800-49455600	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr3:49452000-49455400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:49452000-49455400	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:49452000-49455400	Strong transcription	Osteobl	bone
20	chr3:49452000-49457400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:49452000-49458200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:49452200-49455400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:49452200-49455400	Strong transcription	Aorta	Aorta
24	chr3:49452200-49455400	Strong transcription	Brain Anterior Caudate	brain
25	chr3:49452200-49457800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:49452200-49458000	Strong transcription	Fetal Intestine Large	intestine
27	chr3:49452400-49457000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
28	chr3:49452400-49458400	Strong transcription	Fetal Brain Female	brain
29	chr3:49452800-49455800	Genic enhancers	Fetal Thymus	thymus
30	chr3:49453000-49455400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:49453000-49455600	Genic enhancers	Fetal Muscle Leg	muscle
32	chr3:49453200-49455600	Genic enhancers	Right Ventricle	heart
33	chr3:49453400-49455400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:49453400-49455600	Enhancers	Primary hematopoietic stem cells	blood
35	chr3:49453400-49455600	Genic enhancers	Lung	lung
36	chr3:49453400-49457000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:49453400-49458200	Weak transcription	NH-A	brain
38	chr3:49453400-49458400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr3:49453600-49455800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:49453600-49459000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr3:49453800-49455400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:49453800-49459000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:49454000-49455600	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr3:49454000-49455600	Genic enhancers	A549	lung
45	chr3:49454000-49455800	Strong transcription	Brain Substantia Nigra	brain
46	chr3:49454000-49456400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:49454000-49458200	Strong transcription	Brain Cingulate Gyrus	brain
48	chr3:49454000-49459400	Weak transcription	Brain Angular Gyrus	brain
49	chr3:49454200-49455600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:49454200-49455600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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