Variant report

Variant	rs2223009
Chromosome Location	chr8:90915835-90915836
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:90913673-90916136	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr8:90915817-90916310	MCF10A-Er-Src	breast:	n/a	n/a
3	MXI1	chr8:90913464-90915946	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr8:90913915-90915926	GM12878	blood:	n/a	n/a
5	POLR2A	chr8:90913876-90916292	Hela-S3	cervix:	n/a	n/a
6	CHD1	chr8:90914346-90915903	H1-hESC	embryonic stem cell:	n/a	chr8:90914652-90914662
7	POLR2A	chr8:90913764-90916967	MCF10A-Er-Src	breast:	n/a	n/a
8	CHD1	chr8:90914978-90916739	GM12878	blood:	n/a	n/a
9	POLR2A	chr8:90913892-90916508	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr8:90913406-90916870	K562	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:90767168..90772413-chr8:90911120..90917480,11	K562	blood:
2	chr8:90914281..90916675-chr8:91011002..91013854,2	MCF-7	breast:
3	chr8:90767236..90773457-chr8:90912212..90919638,16	MCF-7	breast:
4	chr8:90915800..90917869-chr8:90927701..90930524,2	K562	blood:
5	chr8:90913353..90915903-chr8:90994626..90998419,6	K562	blood:
6	chr8:90854578..90857222-chr8:90915273..90917997,2	MCF-7	breast:
7	chr8:90914226..90916241-chr8:91996581..91998635,2	K562	blood:
8	chr8:90911185..90916499-chr8:90992960..90998209,20	MCF-7	breast:
9	chr8:90766999..90771986-chr8:90912842..90916534,13	MCF-7	breast:
10	chr8:90913046..90917912-chr8:90949306..90952418,7	MCF-7	breast:
11	chr8:90903994..90907107-chr8:90915784..90918218,3	MCF-7	breast:
12	chr8:90915281..90919071-chr8:91010882..91014336,4	MCF-7	breast:
13	chr8:90912595..90916756-chr8:90994852..90998205,9	K562	blood:
14	chr8:90913489..90916241-chr8:91996581..91998462,2	K562	blood:
15	chr8:90914455..90916377-chr8:91657322..91659594,2	K562	blood:
16	chr8:90913007..90918207-chr8:90995257..90997906,9	MCF-7	breast:

No data

Variant related genes	Relation type
RNU6-925P	TF binding region
ENSG00000253250	Chromatin interaction
ENSG00000104325	Chromatin interaction
ENSG00000104320	Chromatin interaction
ENSG00000246792	Chromatin interaction
ENSG00000251136	Chromatin interaction
ENSG00000104312	Chromatin interaction
ENSG00000180694	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1805796	0.87[YRI][hapmap]
rs2178857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2250670	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2697668	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2697674	1.00[YRI][hapmap]
rs2734823	1.00[YRI][hapmap]
rs2735376	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2735884	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2735888	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs989384	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	esv3371037	chr8:90912579-90917077	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	esv3328681	chr8:90913579-90916277	Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	esv3321826	chr8:90913604-90916152	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2223009	NBN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90912800-90916200	Active TSS	A549	lung
2	chr8:90913200-90916000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr8:90913200-90917200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr8:90913400-90916200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr8:90913400-90916200	Active TSS	HSMMtube	muscle
6	chr8:90913400-90916400	Active TSS	H1 Cell Line	embryonic stem cell
7	chr8:90913400-90916400	Active TSS	Brain Substantia Nigra	brain
8	chr8:90913400-90916600	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr8:90913400-90916800	Active TSS	Brain Anterior Caudate	brain
10	chr8:90913600-90916000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:90913600-90916000	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr8:90913600-90916000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr8:90913600-90916000	Active TSS	GM12878-XiMat	blood
14	chr8:90913600-90916200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr8:90913600-90916200	Active TSS	Fetal Kidney	kidney
16	chr8:90913600-90916400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr8:90913600-90916600	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr8:90913600-90916600	Active TSS	Rectal Smooth Muscle	rectum
19	chr8:90913600-90916600	Active TSS	K562	blood
20	chr8:90913600-90916800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr8:90913600-90917000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr8:90913600-90917000	Active TSS	Stomach Smooth Muscle	stomach
23	chr8:90913800-90916000	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr8:90913800-90916000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr8:90913800-90916000	Active TSS	HepG2	liver
26	chr8:90913800-90916400	Active TSS	Colon Smooth Muscle	Colon
27	chr8:90913800-90916400	Active TSS	HMEC	breast
28	chr8:90913800-90916400	Active TSS	NHLF	lung
29	chr8:90913800-90916600	Active TSS	Hela-S3	cervix
30	chr8:90913800-90916800	Active TSS	Duodenum Mucosa	Duodenum
31	chr8:90913800-90917000	Active TSS	Ovary	ovary
32	chr8:90913800-90917200	Active TSS	Aorta	Aorta
33	chr8:90913800-90917400	Active TSS	Brain Cingulate Gyrus	brain
34	chr8:90914000-90916000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr8:90914000-90916000	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr8:90914000-90916000	Active TSS	NHEK	skin
37	chr8:90914000-90916200	Active TSS	NHDF-Ad	bronchial
38	chr8:90914000-90916600	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr8:90914200-90916000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr8:90914200-90916200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr8:90914200-90916600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr8:90914200-90916800	Active TSS	NH-A	brain
43	chr8:90914400-90916600	Active TSS	Fetal Muscle Leg	muscle
44	chr8:90915200-90916200	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr8:90915400-90916000	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr8:90915400-90916000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr8:90915400-90916200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr8:90915400-90916200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr8:90915400-90916400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr8:90915400-90916400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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