Variant report

Variant	rs2669909
Chromosome Location	chr3:113265727-113265728
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:113232632..113237183-chr3:113263393..113272581,15	MCF-7	breast:
2	chr3:113219243..113222191-chr3:113264588..113266583,2	MCF-7	breast:
3	chr3:113264597..113268411-chr3:113270878..113272522,4	MCF-7	breast:
4	chr3:113231532..113235670-chr3:113264578..113267346,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163611	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11537650	0.89[EUR][1000 genomes]
rs13082603	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs13092925	0.87[EUR][1000 genomes]
rs1463643	0.88[EUR][1000 genomes]
rs1471883	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1471884	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1552433	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16861103	0.95[CEU][hapmap];0.84[GIH][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap]
rs2087130	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs2254267	0.85[MKK][hapmap]
rs2399477	0.95[CEU][hapmap];0.84[GIH][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs2399480	0.89[EUR][1000 genomes]
rs2614191	0.86[MEX][hapmap]
rs4396864	0.94[CEU][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes]
rs60634072	0.82[EUR][1000 genomes]
rs6438160	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6769604	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6783387	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6793704	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72946748	0.83[EUR][1000 genomes]
rs7618226	0.88[EUR][1000 genomes]
rs7623919	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7628945	0.88[EUR][1000 genomes]
rs7631335	0.84[JPT][hapmap];0.88[EUR][1000 genomes]
rs7635676	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7637618	0.95[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7646188	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7650671	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9842559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846539	0.89[EUR][1000 genomes]
rs9852703	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9854686	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870996	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9874747	0.87[EUR][1000 genomes]
rs9877649	0.89[EUR][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	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2669909	BTLA	cis	cerebellum	SCAN
rs2669909	BOC	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113255400-113278800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:113255600-113274800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:113255600-113278400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:113256000-113279000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:113257200-113265800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:113257200-113277400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:113257200-113283400	Weak transcription	Primary B cells from cord blood	blood
8	chr3:113258400-113267600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:113261000-113267400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:113261200-113266800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:113261200-113276200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:113262400-113266400	Weak transcription	Thymus	Thymus
13	chr3:113262400-113272200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr3:113262600-113278800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:113263600-113270000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:113263800-113273000	Weak transcription	Primary T cells from cord blood	blood
17	chr3:113264400-113266800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr3:113264800-113265800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:113265000-113271600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr3:113265200-113265800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr3:113265400-113271400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:113265600-113266800	Flanking Active TSS	GM12878-XiMat	blood
23	chr3:113265600-113267600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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