Variant report

Variant	rs10178850
Chromosome Location	chr2:151022044-151022045
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:151015971..151018361-chr2:151021107..151023162,2	K562	blood:
2	chr2:151018984..151021461-chr2:151021617..151024029,2	K562	blood:
3	chr2:151021749..151023909-chr2:151069571..151071445,2	MCF-7	breast:
4	chr2:151020603..151025476-chr2:151341674..151344465,7	MCF-7	breast:
5	chr2:151018212..151020426-chr2:151020566..151023225,3	MCF-7	breast:
6	chr2:151015440..151017637-chr2:151020964..151024352,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115963	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10180319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10195216	0.98[ASN][1000 genomes]
rs1157219	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11685263	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11687975	0.88[ASN][1000 genomes]
rs11693901	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12618290	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13405415	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1374159	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2376607	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs28871317	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4417736	0.98[ASN][1000 genomes]
rs4567956	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4667375	0.98[ASN][1000 genomes]
rs4667376	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4667377	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4667379	0.98[ASN][1000 genomes]
rs6708312	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6719194	0.95[ASN][1000 genomes]
rs6721152	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6727767	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6727863	0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6750791	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7563665	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7601392	0.98[ASN][1000 genomes]
rs9287808	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs954077	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005441	chr2:150457624-151060247	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv995119	chr2:150556150-151294696	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1001838	chr2:150819672-151745876	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription 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	51 gene(s)	inside rSNPs	diseases
4	nsv535980	chr2:150819672-151745876	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv469524	chr2:150927500-151076920	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv834412	chr2:151014270-151116638	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv523180	chr2:151019241-151022044	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	nsv583294	chr2:151022044-151037893	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10178850	NMI	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151013400-151023800	Weak transcription	Fetal Brain Male	brain
2	chr2:151013800-151022800	Weak transcription	Fetal Lung	lung
3	chr2:151017200-151024000	Weak transcription	NHDF-Ad	bronchial
4	chr2:151018600-151022800	Weak transcription	Aorta	Aorta
5	chr2:151019400-151022600	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:151020200-151022600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:151020400-151022600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:151020400-151022600	Weak transcription	Brain Germinal Matrix	brain
9	chr2:151020400-151022600	Weak transcription	HUVEC	blood vessel
10	chr2:151021400-151022400	Enhancers	A549	lung
11	chr2:151021600-151023200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:151021800-151023200	Enhancers	Stomach Smooth Muscle	stomach
13	chr2:151021800-151023400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:151021800-151023400	Enhancers	Colon Smooth Muscle	Colon
15	chr2:151021800-151026200	Enhancers	NH-A	brain
16	chr2:151021800-151026800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:151022000-151022200	Flanking Active TSS	Liver	Liver
18	chr2:151022000-151022800	Enhancers	K562	blood
19	chr2:151022000-151023600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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