Variant report

Variant	rs9900378
Chromosome Location	chr17:33911302-33911303
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	ATF1	chr17:33911286-33911318	K562	blood:	n/a	n/a
2	TAL1	chr17:33911212-33911421	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:33909950..33911908-chr17:34136327..34138686,2	K562	blood:
2	chr17:33903370..33909494-chr17:33910892..33920548,27	MCF-7	breast:
3	chr17:33910095..33911613-chr17:33912254..33914641,2	MCF-7	breast:

Variant related genes	Relation type
AP2B1	TF binding region
ENSG00000172660	Chromatin interaction
ENSG00000108733	Chromatin interaction
ENSG00000006125	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1001441	0.83[JPT][hapmap]
rs10068	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1037590	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1037592	0.81[ASN][1000 genomes]
rs10512472	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs11080357	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11653310	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11653357	0.84[ASN][1000 genomes]
rs11655803	0.83[ASN][1000 genomes]
rs11656138	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452797	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs12604067	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12947592	0.81[ASN][1000 genomes]
rs12948669	0.84[ASN][1000 genomes]
rs1671656	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16971217	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16971227	0.83[ASN][1000 genomes]
rs17637907	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs225243	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225247	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225259	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225262	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225285	0.90[CEU][hapmap]
rs225295	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225304	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225306	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.99[ASN][1000 genomes]
rs2840044	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28667378	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35237539	0.84[ASN][1000 genomes]
rs7212704	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8069037	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8073935	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9890191	0.81[ASN][1000 genomes]
rs9891574	0.81[ASN][1000 genomes]
rs9891800	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9897552	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9899860	0.82[ASN][1000 genomes]
rs9899927	0.82[ASN][1000 genomes]
rs9902765	0.82[ASN][1000 genomes]
rs9908158	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9913003	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9913875	0.82[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	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33906400-33913800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:33906400-33913800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:33906600-33913400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr17:33906600-33913400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr17:33906600-33913400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:33906600-33913400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:33906600-33913400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr17:33906600-33913400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr17:33906600-33913400	Weak transcription	Liver	Liver
10	chr17:33906600-33913400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr17:33906600-33913400	Weak transcription	NHEK	skin
12	chr17:33906600-33913800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr17:33906600-33914000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr17:33906800-33913600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr17:33907200-33913600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr17:33907200-33913800	Weak transcription	HepG2	liver
17	chr17:33907400-33911400	Weak transcription	K562	blood
18	chr17:33909600-33913400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr17:33910600-33912000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr17:33910600-33912000	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr17:33911000-33911400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr17:33911000-33911800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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