Variant report

Variant	rs1036769
Chromosome Location	chr3:100122081-100122082
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr3:100118890-100122089	Hela-S3	cervix:	n/a	n/a
2	MXI1	chr3:100118433-100122085	IMR90	lung:	n/a	n/a
3	MXI1	chr3:100118461-100122114	SK-N-SH	brain:	n/a	n/a
4	CHD1	chr3:100119941-100122591	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZNF384	chr3:100121195-100122588	K562	blood:	n/a	n/a
6	GATA3	chr3:100121002-100122217	SH-SY5Y	brain:	n/a	n/a
7	YY1	chr3:100121835-100122780	SK-N-SH	brain:	n/a	chr3:100122366-100122378

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:100120411..100122999-chr3:100364924..100367578,2	K562	blood:
2	chr3:100120464..100122813-chr3:100141808..100145050,3	K562	blood:
3	chr17:57182962..57185099-chr3:100120179..100122851,2	MCF-7	breast:
4	chr3:100097916..100106101-chr3:100115627..100122137,10	K562	blood:
5	chr3:99535287..99537035-chr3:100119228..100122105,2	MCF-7	breast:
6	chr3:100120818..100123698-chr3:100370041..100372201,2	K562	blood:
7	chr3:100052434..100055247-chr3:100118351..100122265,5	K562	blood:

No data

Variant related genes	Relation type
TOMM70A	TF binding region
ENSG00000224738	Chromatin interaction
ENSG00000252989	Chromatin interaction
ENSG00000114021	Chromatin interaction
ENSG00000184220	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000154174	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11711112	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[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1214374	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12696105	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[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2119686	0.80[AMR][1000 genomes]
rs2289503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289504	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2316701	0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs277621	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277627	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs277631	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277646	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277648	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277649	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs378535	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs421855	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4928171	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781422	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6784494	0.95[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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1036769	LNP1	cis	Muscle Skeletal	GTEx
rs1036769	NIT2	cis	parietal	SCAN
rs1036769	RG9MTD1	cis	parietal	SCAN
rs1036769	LOC348801	Cis_1M	lymphoblastoid	RTeQTL
rs1036769	LNP1	cis	Esophagus Muscularis	GTEx
rs1036769	LNP1	cis	Thyroid	GTEx
rs1036769	C3orf26	cis	cerebellum	SCAN
rs1036769	NIT2	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100117000-100123000	Active TSS	K562	blood
2	chr3:100117800-100122800	Active TSS	Right Atrium	heart
3	chr3:100118200-100122400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:100118200-100122400	Active TSS	HSMMtube	muscle
5	chr3:100118200-100122600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr3:100118200-100122600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:100118200-100123400	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr3:100118200-100123600	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr3:100118400-100122600	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr3:100118400-100122600	Active TSS	Fetal Intestine Large	intestine
11	chr3:100118400-100122600	Active TSS	NHDF-Ad	bronchial
12	chr3:100118400-100123000	Active TSS	H1 Cell Line	embryonic stem cell
13	chr3:100118400-100123000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:100118400-100123000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr3:100118400-100123000	Active TSS	NHLF	lung
16	chr3:100118600-100123000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr3:100118800-100122200	Active TSS	Fetal Lung	lung
18	chr3:100118800-100122200	Active TSS	Fetal Stomach	stomach
19	chr3:100118800-100122400	Active TSS	Colonic Mucosa	Colon
20	chr3:100118800-100122600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:100118800-100122600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:100118800-100122600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:100118800-100123000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:100118800-100123400	Active TSS	GM12878-XiMat	blood
25	chr3:100119000-100122200	Active TSS	Fetal Muscle Trunk	muscle
26	chr3:100119000-100122200	Active TSS	Hela-S3	cervix
27	chr3:100119000-100122600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr3:100119000-100122600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:100119000-100122800	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr3:100119000-100122800	Active TSS	Pancreas	Pancrea
31	chr3:100119000-100123000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:100119000-100123200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:100119000-100123200	Active TSS	Fetal Brain Female	brain
34	chr3:100119200-100122400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:100119200-100122600	Active TSS	Liver	Liver
36	chr3:100119200-100122800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:100119200-100123200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:100119200-100124600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:100119400-100122200	Active TSS	Brain Angular Gyrus	brain
40	chr3:100119400-100122600	Active TSS	Brain Cingulate Gyrus	brain
41	chr3:100119400-100123000	Active TSS	Stomach Smooth Muscle	stomach
42	chr3:100119600-100122600	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr3:100120000-100122600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:100120400-100122400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:100120400-100123000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:100120800-100122600	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr3:100121000-100123200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:100121000-100127000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:100121000-100127000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:100121000-100127000	Weak transcription	Gastric	stomach

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