Variant report

Variant	rs277621
Chromosome Location	chr3:100057203-100057204
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	chr3:100056720-100057772	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:100055925..100057917-chr3:100076174..100079116,2	MCF-7	breast:
2	chr3:100051539..100055958-chr3:100056037..100061247,9	MCF-7	breast:
3	chr3:100056838..100058599-chr3:100119834..100121558,2	MCF-7	breast:

Variant related genes	Relation type
NIT2	TF binding region
ENSG00000206535	Chromatin interaction
ENSG00000114021	Chromatin interaction
ENSG00000154174	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1036769	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]
rs11711112	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1214374	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12696105	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289503	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289504	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277627	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs277631	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277640	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277646	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277648	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277649	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378535	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs421855	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4928171	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781422	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6784494	1.00[ASN][1000 genomes]

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	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
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv3387925	chr3:100056362-100059860	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs277621	LNP1	cis	Esophagus Muscularis	GTEx
rs277621	TBC1D23	cis	Muscle Skeletal	GTEx
rs277621	LNP1	cis	Muscle Skeletal	GTEx
rs277621	C3orf26	cis	cerebellum	SCAN
rs277621	RG9MTD1	cis	parietal	SCAN
rs277621	NIT2	cis	parietal	SCAN
rs277621	NIT2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054000-100065000	Weak transcription	Spleen	Spleen
2	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:100054400-100067600	Weak transcription	Psoas Muscle	Psoas
4	chr3:100054600-100057400	Weak transcription	Primary T cells from cord blood	blood
5	chr3:100054600-100058000	Weak transcription	Fetal Brain Male	brain
6	chr3:100054600-100058000	Weak transcription	Fetal Brain Female	brain
7	chr3:100054600-100058200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:100054600-100058400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:100054600-100058600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:100054600-100058600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:100054600-100058800	Weak transcription	Aorta	Aorta
12	chr3:100054600-100059400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:100054600-100059800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:100054600-100060200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:100054600-100063000	Weak transcription	Brain Substantia Nigra	brain
16	chr3:100054600-100064200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:100054600-100064400	Weak transcription	Thymus	Thymus
18	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr3:100054800-100057400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:100054800-100057400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr3:100054800-100057600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:100054800-100057600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:100054800-100057600	Weak transcription	Adipose Nuclei	Adipose
24	chr3:100054800-100057600	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:100054800-100057600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:100054800-100057800	Enhancers	Liver	Liver
27	chr3:100054800-100057800	Weak transcription	Gastric	stomach
28	chr3:100054800-100057800	Weak transcription	Ovary	ovary
29	chr3:100054800-100057800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:100054800-100057800	Weak transcription	NHDF-Ad	bronchial
31	chr3:100054800-100058000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr3:100054800-100058000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:100054800-100058000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:100054800-100058000	Weak transcription	Fetal Thymus	thymus
35	chr3:100054800-100058000	Weak transcription	Left Ventricle	heart
36	chr3:100054800-100058000	Weak transcription	Lung	lung
37	chr3:100054800-100058000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:100054800-100058000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:100054800-100058000	Weak transcription	HSMMtube	muscle
40	chr3:100054800-100058400	Weak transcription	NH-A	brain
41	chr3:100054800-100058600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:100054800-100058600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:100054800-100058800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:100054800-100058800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:100054800-100059400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr3:100054800-100059400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:100054800-100060000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:100054800-100060000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:100054800-100060200	Weak transcription	Right Ventricle	heart
50	chr3:100054800-100060600	Weak transcription	Rectal Mucosa Donor 31	rectum

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