Variant report

Variant	rs9865051
Chromosome Location	chr3:49166069-49166070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49165978-49166171	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49157786..49160354-chr3:49162169..49166398,5	MCF-7	breast:
2	chr3:49129337..49131574-chr3:49165635..49167419,2	K562	blood:
3	chr3:49130549..49132053-chr3:49166037..49168873,2	MCF-7	breast:
4	chr3:49165625..49169555-chr3:49201131..49204246,4	MCF-7	breast:
5	chr3:49158149..49166168-chr3:49166363..49171688,12	K562	blood:

No data

Variant related genes	Relation type
LAMB2	TF binding region
ENSG00000177352	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000172037	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 33 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10154992	0.91[CEU][hapmap]
rs11130181	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11130183	0.87[CEU][hapmap]
rs11130186	0.83[CEU][hapmap]
rs11540500	1.00[CHD][hapmap]
rs13084037	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs13099075	0.91[AMR][1000 genomes]
rs28673107	1.00[CHD][hapmap]
rs3087866	1.00[ASW][hapmap];0.86[CEU][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs35806761	1.00[JPT][hapmap]
rs35867420	1.00[CHD][hapmap]
rs4292260	1.00[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4955411	1.00[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4955416	0.95[CEU][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4955417	0.91[CEU][hapmap]
rs4955426	1.00[CEU][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4955439	0.87[CEU][hapmap];0.82[TSI][hapmap]
rs4955443	0.91[CEU][hapmap]
rs4974081	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs4974083	0.95[CEU][hapmap];0.93[TSI][hapmap]
rs6446204	0.95[CEU][hapmap];0.93[TSI][hapmap]
rs6446247	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6446256	0.90[CEU][hapmap]
rs6446257	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs6769821	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs6772452	0.95[CEU][hapmap];0.90[TSI][hapmap]
rs6778080	0.91[CEU][hapmap];0.82[TSI][hapmap]
rs6787808	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs6798112	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6803264	0.88[EUR][1000 genomes]
rs6809851	0.91[CEU][hapmap];0.82[TSI][hapmap]
rs7100	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs7429661	0.87[CEU][hapmap];0.82[TSI][hapmap]
rs7434187	0.84[ASW][hapmap];0.95[CEU][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs7617480	0.82[TSI][hapmap]
rs7619016	0.91[CEU][hapmap];0.82[TSI][hapmap]
rs7621347	0.82[AMR][1000 genomes]
rs7626076	0.91[CEU][hapmap];0.82[TSI][hapmap]
rs7653408	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs9586	0.82[TSI][hapmap]
rs9831648	0.82[TSI][hapmap]
rs9834003	0.87[CEU][hapmap]
rs9864243	1.00[ASW][hapmap];0.95[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap]
rs9881860	0.91[CEU][hapmap]

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	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:33)

SNP	Gene	Cis/trans	Tissue	Source
rs9865051	AMT	cis	lung	GTEx
rs9865051	NCKIPSD	cis	Nerve Tibial	GTEx
rs9865051	WDR6	cis	parietal	SCAN
rs9865051	AMT	cis	parietal	SCAN
rs9865051	AMT	cis	cerebellum	SCAN
rs9865051	AMT	cis	Artery Aorta	GTEx
rs9865051	AMT	cis	Whole Blood	GTEx
rs9865051	NICN1	cis	cerebellum	SCAN
rs9865051	ZNF589	cis	parietal	SCAN
rs9865051	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs9865051	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs9865051	PHF7	cis	parietal	SCAN
rs9865051	WDR6	cis	cerebellum	SCAN
rs9865051	P4HTM	cis	parietal	SCAN
rs9865051	DALRD3	cis	parietal	SCAN
rs9865051	WDR6	cis	Nerve Tibial	GTEx
rs9865051	AMT	cis	Thyroid	GTEx
rs9865051	AMT	cis	Muscle Skeletal	GTEx
rs9865051	LZTFL1	cis	cerebellum	SCAN
rs9865051	TLR9	cis	parietal	SCAN
rs9865051	IQCF1	cis	cerebellum	SCAN
rs9865051	NICN1	cis	parietal	SCAN
rs9865051	NICN1-AS1	cis	Thyroid	GTEx
rs9865051	NICN1	cis	Thyroid	GTEx
rs9865051	WDR6	cis	Muscle Skeletal	GTEx
rs9865051	AMT	cis	lymphoblastoid	seeQTL
rs9865051	GPX1	cis	parietal	SCAN
rs9865051	AMT	cis	Artery Tibial	GTEx
rs9865051	DALRD3	cis	cerebellum	SCAN
rs9865051	AMT	cis	Adipose Subcutaneous	GTEx
rs9865051	QRICH1	cis	cerebellum	SCAN
rs9865051	AMT	cis	Nerve Tibial	GTEx
rs9865051	NCKIPSD	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49158200-49169600	Weak transcription	Fetal Brain Male	brain
2	chr3:49158400-49169200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:49158600-49166600	Strong transcription	Aorta	Aorta
4	chr3:49158600-49167200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:49158600-49167600	Strong transcription	Gastric	stomach
6	chr3:49158600-49168600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:49158600-49168600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:49158600-49168800	Strong transcription	Osteobl	bone
9	chr3:49158800-49166600	Strong transcription	Fetal Lung	lung
10	chr3:49158800-49167000	Strong transcription	Left Ventricle	heart
11	chr3:49158800-49167800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:49158800-49168000	Strong transcription	Fetal Stomach	stomach
13	chr3:49158800-49168400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:49158800-49168400	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr3:49158800-49168600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:49158800-49168800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:49158800-49169200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:49158800-49169200	Weak transcription	Brain Germinal Matrix	brain
19	chr3:49158800-49169400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:49159000-49166800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr3:49159000-49167000	Strong transcription	Placenta	Placenta
22	chr3:49159000-49167600	Strong transcription	Adipose Nuclei	Adipose
23	chr3:49159000-49167800	Strong transcription	Colon Smooth Muscle	Colon
24	chr3:49159000-49168400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:49159000-49169000	Strong transcription	Fetal Intestine Small	intestine
26	chr3:49159000-49169200	Weak transcription	Brain Angular Gyrus	brain
27	chr3:49159000-49169400	Weak transcription	Fetal Brain Female	brain
28	chr3:49159000-49170000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:49159200-49166600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:49159200-49167400	Strong transcription	Fetal Muscle Leg	muscle
31	chr3:49159200-49168800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:49159200-49169000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:49159400-49166600	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:49159400-49169200	Strong transcription	Fetal Intestine Large	intestine
35	chr3:49160000-49168000	Strong transcription	Ovary	ovary
36	chr3:49161400-49169200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:49161600-49167400	Weak transcription	Fetal Heart	heart
38	chr3:49162200-49169000	Weak transcription	A549	lung
39	chr3:49162400-49169200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:49162400-49169400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:49162400-49169400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr3:49162400-49169400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:49162600-49168200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:49162600-49168200	Weak transcription	Psoas Muscle	Psoas
45	chr3:49162600-49169200	Weak transcription	Stomach Mucosa	stomach
46	chr3:49162600-49169400	Weak transcription	Brain Hippocampus Middle	brain
47	chr3:49162800-49167000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr3:49163000-49166200	Weak transcription	Brain Anterior Caudate	brain
49	chr3:49163000-49169400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:49163200-49167400	Strong transcription	NH-A	brain

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