Variant report

Variant	rs3758253
Chromosome Location	chr9:100700654-100700655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100698882..100701716-chr9:100722332..100724785,2	K562	blood:
2	chr9:100698423..100701037-chr9:100720373..100724214,5	K562	blood:
3	chr9:100700511..100703387-chr9:100744049..100746713,2	MCF-7	breast:
4	chr9:100678422..100708679-chr9:100734559..100755577,174	K562	blood:
5	chr9:100697884..100704099-chr9:100714128..100720073,9	K562	blood:
6	chr9:100698192..100700969-chr9:100818656..100820847,3	K562	blood:
7	chr9:100675954..100709047-chr9:100737887..100755543,175	K562	blood:

No data

Variant related genes	Relation type
ENSG00000136938	Chromatin interaction
ENSG00000236896	Chromatin interaction
ENSG00000095380	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10119795	0.81[CHB][hapmap]
rs10760021	0.93[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760022	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984361	1.00[CEU][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10984373	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10984405	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10984466	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10984499	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10984506	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12238579	0.81[CHB][hapmap]
rs12377604	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1475695	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1475696	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1561958	0.81[CHB][hapmap]
rs17431614	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17431934	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2120263	0.94[CHB][hapmap];0.92[ASN][1000 genomes]
rs2282192	0.94[CHB][hapmap];0.92[ASN][1000 genomes]
rs2417577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3183927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3183928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3758254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3808894	0.92[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3824496	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4631576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743145	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4743147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55737216	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586	0.81[CHB][hapmap]
rs66990486	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7030887	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7030907	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs755109	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7861658	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7864655	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1048135	chr9:100666931-100717030	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3758253	Hs.43687	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100697200-100701600	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr9:100697400-100701600	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr9:100699200-100701600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr9:100699400-100701400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr9:100700000-100700800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:100700000-100701200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr9:100700000-100701400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr9:100700000-100701600	Enhancers	Dnd41	blood
9	chr9:100700200-100700800	Enhancers	Primary T cells from cord blood	blood
10	chr9:100700200-100700800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr9:100700200-100700800	Flanking Active TSS	Thymus	Thymus
12	chr9:100700200-100701000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr9:100700400-100700800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr9:100700400-100700800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:100700400-100701000	Enhancers	Primary B cells from peripheral blood	blood
16	chr9:100700400-100707000	Enhancers	Primary hematopoietic stem cells	blood
17	chr9:100700600-100700800	Bivalent Enhancer	Lung	lung
18	chr9:100700600-100700800	Flanking Active TSS	K562	blood
19	chr9:100700600-100701000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr9:100700600-100701000	Enhancers	Fetal Thymus	thymus
21	chr9:100700600-100701000	Flanking Active TSS	GM12878-XiMat	blood
22	chr9:100700600-100701400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr9:100700600-100701600	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr9:100700600-100701600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr9:100700600-100706800	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr9:100700600-100707000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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