Variant report

Variant	rs4292260
Chromosome Location	chr3:49148890-49148891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49148759-49149008	K562	blood:	n/a	n/a
2	POLR2A	chr3:49148786-49149589	GM12878	blood:	n/a	n/a
3	NFIC	chr3:49148732-49149197	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49141824..49144900-chr3:49147754..49149613,4	K562	blood:
2	chr3:49128926..49138937-chr3:49145476..49160975,31	K562	blood:
3	chr3:49148095..49150298-chr3:49155546..49158481,2	K562	blood:
4	chr3:49137640..49139439-chr3:49147793..49150282,2	K562	blood:
5	chr3:49131330..49133492-chr3:49146918..49149870,2	MCF-7	breast:
6	chr3:49146749..49150327-chr3:49159131..49161330,3	K562	blood:
7	chr3:49130002..49134881-chr3:49145556..49149434,6	K562	blood:
8	chr3:49148001..49150538-chr3:49150834..49154953,4	K562	blood:
9	chr3:49136200..49139110-chr3:49147994..49150286,3	MCF-7	breast:
10	chr3:49144707..49154191-chr3:49155059..49160099,12	MCF-7	breast:

No data

Variant related genes	Relation type
USP19	TF binding region
ENSG00000198218	Chromatin interaction
ENSG00000172053	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000172046	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 38 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10154992	0.81[ASW][hapmap];0.91[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs11130181	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11130183	0.81[ASW][hapmap];0.87[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap]
rs11130186	0.81[ASW][hapmap];0.83[CEU][hapmap];0.82[TSI][hapmap]
rs1134591	0.82[YRI][hapmap]
rs13099075	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3087866	0.86[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs3212	0.86[YRI][hapmap]
rs4364202	0.83[AFR][1000 genomes]
rs4521268	0.82[YRI][hapmap]
rs4955411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][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]
rs4955416	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4955417	0.91[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.81[YRI][hapmap]
rs4955421	0.85[YRI][hapmap]
rs4955426	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs4955439	0.87[CEU][hapmap]
rs4955443	0.91[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.81[YRI][hapmap]
rs4974080	0.86[YRI][hapmap]
rs4974081	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs4974083	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs6446196	0.81[ASW][hapmap];0.86[YRI][hapmap]
rs6446204	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs6446205	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs6446247	0.85[AMR][1000 genomes]
rs6446256	0.90[CEU][hapmap];0.84[YRI][hapmap]
rs6446257	0.86[CEU][hapmap]
rs6769821	0.87[CEU][hapmap]
rs6772452	0.95[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs6778080	0.91[CEU][hapmap];0.83[MEX][hapmap]
rs6779394	0.81[ASW][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs6781790	0.82[YRI][hapmap]
rs6787808	0.95[CEU][hapmap]
rs6798112	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6803264	0.88[EUR][1000 genomes]
rs6809851	0.91[CEU][hapmap];0.83[MEX][hapmap]
rs7100	0.86[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs7373072	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs7373790	0.86[AFR][1000 genomes]
rs7429661	0.87[CEU][hapmap]
rs7430198	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs7432989	0.81[ASW][hapmap];0.93[YRI][hapmap]
rs7434187	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs7617480	0.93[ASW][hapmap];0.98[LWK][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs7619016	0.91[CEU][hapmap]
rs7621015	0.82[YRI][hapmap]
rs7621347	0.81[EUR][1000 genomes]
rs7626076	0.91[CEU][hapmap]
rs7626445	0.82[YRI][hapmap]
rs7643368	0.82[YRI][hapmap]
rs7653408	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs9586	0.87[ASW][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs9637481	0.89[YRI][hapmap]
rs9831648	0.87[ASW][hapmap];0.98[LWK][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9834003	0.81[ASW][hapmap];0.87[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap]
rs9840050	0.86[YRI][hapmap]
rs9846123	0.82[YRI][hapmap]
rs9864243	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs9865051	1.00[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9884022	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv876765	chr3:49119063-49160671	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:38)

SNP	Gene	Cis/trans	Tissue	Source
rs4292260	WDR6	cis	lymphoblastoid	seeQTL
rs4292260	QRICH1	cis	Nerve Tibial	GTEx
rs4292260	AMT	cis	lymphoblastoid	seeQTL
rs4292260	NICN1	cis	parietal	SCAN
rs4292260	AMT	cis	Muscle Skeletal	GTEx
rs4292260	AMT	cis	Artery Aorta	GTEx
rs4292260	WDR6	cis	Nerve Tibial	GTEx
rs4292260	PHF7	cis	parietal	SCAN
rs4292260	AMT	cis	Thyroid	GTEx
rs4292260	AMT	cis	lung	GTEx
rs4292260	AMT	cis	parietal	SCAN
rs4292260	NICN1	cis	cerebellum	SCAN
rs4292260	IQCF1	cis	cerebellum	SCAN
rs4292260	DALRD3	cis	cerebellum	SCAN
rs4292260	DALRD3	cis	parietal	SCAN
rs4292260	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs4292260	NCKIPSD	cis	parietal	SCAN
rs4292260	AMT	cis	cerebellum	SCAN
rs4292260	AMT	cis	Whole Blood	GTEx
rs4292260	AMT	cis	Nerve Tibial	GTEx
rs4292260	WDR6	cis	Heart Left Ventricle	GTEx
rs4292260	WDR6	cis	Muscle Skeletal	GTEx
rs4292260	LZTFL1	cis	cerebellum	SCAN
rs4292260	P4HTM	cis	parietal	SCAN
rs4292260	TLR9	cis	parietal	SCAN
rs4292260	GPX1	cis	parietal	SCAN
rs4292260	NICN1-AS1	cis	Thyroid	GTEx
rs4292260	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs4292260	AMT	cis	Artery Tibial	GTEx
rs4292260	WDR6	cis	cerebellum	SCAN
rs4292260	WDR6	cis	parietal	SCAN
rs4292260	QRICH1	cis	cerebellum	SCAN
rs4292260	WDR6	cis	lung	GTEx
rs4292260	NCKIPSD	cis	Nerve Tibial	GTEx
rs4292260	NICN1	cis	Thyroid	GTEx
rs4292260	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs4292260	ZNF589	cis	parietal	SCAN
rs4292260	AMT	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49142800-49149000	Weak transcription	NHDF-Ad	bronchial
2	chr3:49142800-49149600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:49142800-49156400	Weak transcription	Right Atrium	heart
4	chr3:49142800-49157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:49142800-49157600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:49143000-49153800	Weak transcription	Fetal Brain Male	brain
7	chr3:49143600-49155200	Strong transcription	Brain Cingulate Gyrus	brain
8	chr3:49143600-49156200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:49143600-49156200	Strong transcription	Brain Anterior Caudate	brain
10	chr3:49143600-49156200	Strong transcription	NHLF	lung
11	chr3:49143600-49156400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:49143600-49156400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:49143600-49156400	Strong transcription	Placenta	Placenta
14	chr3:49143600-49156400	Strong transcription	Fetal Stomach	stomach
15	chr3:49143600-49156400	Strong transcription	NHEK	skin
16	chr3:49143600-49156600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:49143600-49156600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:49143600-49156600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:49143600-49156600	Strong transcription	Fetal Thymus	thymus
20	chr3:49143600-49156800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:49143800-49149600	Weak transcription	Fetal Heart	heart
22	chr3:49143800-49155000	Strong transcription	Adipose Nuclei	Adipose
23	chr3:49143800-49155600	Strong transcription	Esophagus	oesophagus
24	chr3:49143800-49155800	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:49143800-49156200	Strong transcription	Liver	Liver
26	chr3:49143800-49156200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:49143800-49156400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:49143800-49156600	Strong transcription	Fetal Muscle Leg	muscle
29	chr3:49143800-49156600	Strong transcription	Osteobl	bone
30	chr3:49144000-49153000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:49144000-49155000	Strong transcription	Stomach Smooth Muscle	stomach
32	chr3:49144000-49155600	Strong transcription	Brain Angular Gyrus	brain
33	chr3:49144000-49156200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:49144000-49156200	Strong transcription	Brain Germinal Matrix	brain
35	chr3:49144000-49156400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:49144000-49156800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:49144200-49156400	Strong transcription	Gastric	stomach
38	chr3:49144200-49156400	Strong transcription	Lung	lung
39	chr3:49144200-49156800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:49144600-49154000	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:49144600-49155200	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr3:49144600-49155800	Strong transcription	Rectal Smooth Muscle	rectum
43	chr3:49144600-49156400	Strong transcription	Fetal Brain Female	brain
44	chr3:49144600-49156400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr3:49144600-49156600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:49144600-49156600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr3:49144800-49155000	Strong transcription	Colon Smooth Muscle	Colon
48	chr3:49144800-49155000	Strong transcription	Right Ventricle	heart
49	chr3:49144800-49155600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:49144800-49155600	Strong transcription	H9 Cell Line	embryonic stem cell

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