Variant report

Variant	rs9858213
Chromosome Location	chr3:49731861-49731862
allele	G/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	chr3:49731514-49732420	K562	blood:	n/a	n/a
2	SIX5	chr3:49731805-49732122	K562	blood:	n/a	n/a
3	POLR2A	chr3:49731827-49732626	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:16964923..16974624-chr3:49722461..49732046,16	K562	blood:
2	chr1:16965534..16967536-chr3:49731368..49733406,2	MCF-7	breast:

Variant related genes	Relation type
MST1	TF binding region
ENSG00000215908	Chromatin interaction
ENSG00000186301	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1060962	1.00[JPT][hapmap]
rs11130213	0.85[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs1131095	0.85[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs11709525	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap]
rs11718165	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs13085791	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs1801143	0.89[CEU][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap]
rs1873625	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap]
rs2131104	1.00[JPT][hapmap]
rs2131109	1.00[JPT][hapmap]
rs2172252	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs3197999	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap]
rs34762726	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs3811697	0.89[CEU][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap]
rs4283605	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs4625	0.89[CEU][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap]
rs4855884	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6766131	0.89[CEU][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap]
rs6770670	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs6803222	0.85[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs7622302	0.83[ASW][hapmap];0.89[CEU][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap]
rs7633271	0.89[CEU][hapmap]
rs9811982	0.89[CEU][hapmap]
rs9812791	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs9822268	0.89[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs9823546	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs9827708	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs9837027	0.89[CEU][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap]
rs9837341	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs9852529	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9858280	0.89[CEU][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap]
rs9858542	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs9875617	0.89[CEU][hapmap];0.81[GIH][hapmap];0.94[MEX][hapmap]
rs9882740	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv820990	chr3:49720651-49735911	Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv12377	chr3:49720751-49735851	Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	nsv822077	chr3:49721400-49734526	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	esv1825475	chr3:49722732-49734243	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
9	esv11181	chr3:49726377-49733587	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Educational attainment	25201988	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9858213	FAM212A	cis	Muscle Skeletal	GTEx
rs9858213	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9858213	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs9858213	IP6K1	cis	brain	BrainEAC

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49727600-49734600	Weak transcription	Aorta	Aorta
2	chr3:49727600-49734600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:49727800-49736200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:49727800-49740000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:49727800-49742200	Weak transcription	Small Intestine	intestine
6	chr3:49728000-49734400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:49728000-49734600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:49728000-49734600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:49728000-49734600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:49728000-49734800	Weak transcription	Osteobl	bone
11	chr3:49728000-49736200	Weak transcription	HSMMtube	muscle
12	chr3:49728000-49737000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:49728000-49738400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:49728000-49738600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:49728000-49738600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:49728000-49739200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:49728000-49739200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:49728000-49739400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:49728000-49742600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:49728000-49744400	Weak transcription	NH-A	brain
21	chr3:49728000-49748800	Weak transcription	A549	lung
22	chr3:49728400-49734400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:49728400-49734400	Weak transcription	Fetal Brain Female	brain
24	chr3:49728400-49734600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:49728400-49734600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:49728400-49735200	Weak transcription	GM12878-XiMat	blood
27	chr3:49728400-49735600	Weak transcription	NHLF	lung
28	chr3:49728400-49736200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:49728400-49753200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:49728400-49756600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:49728600-49733600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:49728600-49733800	Weak transcription	HUVEC	blood vessel
33	chr3:49728600-49734200	Weak transcription	NHEK	skin
34	chr3:49728600-49734400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:49728600-49734400	Weak transcription	Fetal Lung	lung
36	chr3:49728600-49734600	Weak transcription	Brain Germinal Matrix	brain
37	chr3:49728600-49734600	Weak transcription	Placenta	Placenta
38	chr3:49728600-49735200	Weak transcription	Stomach Mucosa	stomach
39	chr3:49728600-49736200	Weak transcription	HSMM	muscle
40	chr3:49728600-49739400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr3:49728600-49744800	Weak transcription	HMEC	breast
42	chr3:49728600-49750400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:49728800-49732400	Weak transcription	Fetal Heart	heart
44	chr3:49728800-49734400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:49728800-49734400	Weak transcription	Brain Hippocampus Middle	brain
46	chr3:49728800-49734400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:49728800-49734800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:49728800-49735000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:49728800-49735200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr3:49728800-49735400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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