Variant report

Variant	rs2625288
Chromosome Location	chr3:101545319-101545320
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	STAT3	chr3:101545265-101545344	MCF10A-Er-Src	breast:	n/a	n/a
2	NFIC	chr3:101544892-101545532	GM12878	blood:	n/a	n/a
3	EBF1	chr3:101544864-101545589	GM12878	blood:	n/a	n/a
4	ZNF143	chr3:101545069-101545361	GM12878	blood:	n/a	n/a
5	BHLHE40	chr3:101545254-101545766	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:101539582..101541974-chr3:101545076..101546641,2	K562	blood:
2	chr3:101543661..101554550-chr3:101566310..101574179,30	MCF-7	breast:
3	chr3:101544475..101550800-chr3:101565965..101572617,10	K562	blood:

Variant related genes	Relation type
NFKBIZ	TF binding region
ENSG00000249474	TF binding region
ENSG00000144802	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs13065650	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2466368	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2466373	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2554962	0.84[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2611837	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2722163	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34371613	0.83[EUR][1000 genomes]
rs35280358	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3806652	0.82[EUR][1000 genomes]
rs4683854	0.93[CEU][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs595230	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs604521	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68076712	0.81[EUR][1000 genomes]
rs7632449	0.84[YRI][hapmap]
rs771326	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2625288	NXPE3	cis	Whole Blood	GTEx
rs2625288	CBLB	cis	cerebellum	SCAN
rs2625288	NIT2	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101498800-101546200	Weak transcription	Esophagus	oesophagus
2	chr3:101504800-101546000	Weak transcription	Colonic Mucosa	Colon
3	chr3:101515400-101546000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:101516000-101546000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:101520400-101546000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:101520800-101546400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:101521200-101546200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:101528600-101546000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:101534000-101546000	Weak transcription	Fetal Kidney	kidney
10	chr3:101534600-101546000	Weak transcription	Fetal Intestine Large	intestine
11	chr3:101535800-101546200	Weak transcription	Placenta	Placenta
12	chr3:101536400-101546000	Weak transcription	Fetal Brain Male	brain
13	chr3:101536400-101546000	Weak transcription	Psoas Muscle	Psoas
14	chr3:101536800-101546600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:101537000-101546000	Weak transcription	Right Ventricle	heart
16	chr3:101539800-101548000	Weak transcription	Hela-S3	cervix
17	chr3:101540600-101546000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:101540800-101546000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:101540800-101546000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:101540800-101546000	Weak transcription	Aorta	Aorta
21	chr3:101540800-101546000	Weak transcription	Brain Anterior Caudate	brain
22	chr3:101540800-101546000	Weak transcription	Fetal Stomach	stomach
23	chr3:101540800-101546000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:101540800-101546200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:101540800-101546200	Weak transcription	Ovary	ovary
26	chr3:101540800-101546200	Weak transcription	Pancreas	Pancrea
27	chr3:101540800-101546400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:101540800-101546400	Weak transcription	Lung	lung
29	chr3:101540800-101546400	Weak transcription	Spleen	Spleen
30	chr3:101540800-101546600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:101541000-101545400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:101541000-101545400	Weak transcription	Adipose Nuclei	Adipose
33	chr3:101541000-101546000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:101541000-101546000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:101541000-101546000	Weak transcription	Brain Germinal Matrix	brain
36	chr3:101541000-101546000	Weak transcription	HSMMtube	muscle
37	chr3:101541000-101546200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr3:101541000-101546200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:101541000-101546400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:101541000-101548000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:101541200-101546000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:101541200-101546000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:101541200-101546000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:101541200-101546000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:101541200-101546000	Weak transcription	Primary T cells from cord blood	blood
46	chr3:101541200-101546000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:101541200-101546000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:101541200-101546000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:101541200-101546000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:101541200-101546000	Weak transcription	Fetal Lung	lung

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