Variant report

Variant	rs1869002
Chromosome Location	chr11:3870463-3870464
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr11:3855443..3857782-chr11:3869074..3871909,2	K562	blood:
2	chr11:3870169..3871185-chr11:4093536..4094651,4	MCF-7	breast:
3	chr11:3862990..3867083-chr11:3867871..3871459,5	K562	blood:
4	chr11:3869715..3872142-chr11:4092471..4094977,3	K562	blood:
5	chr11:3870263..3871130-chr11:4093603..4094548,6	K562	blood:
6	chr11:3865876..3872194-chr11:3872443..3878070,9	K562	blood:
7	chr11:3870179..3871112-chr11:3980205..3980923,2	K562	blood:
8	chr11:3868931..3871708-chr11:3879201..3881695,3	K562	blood:
9	chr11:3858681..3862774-chr11:3867333..3870611,5	K562	blood:
10	chr11:3869518..3871179-chr11:3872490..3875358,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000167323	Chromatin interaction
ENSG00000228661	Chromatin interaction
ENSG00000177105	Chromatin interaction
ENSG00000229368	Chromatin interaction
ENSG00000263421	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10835184	0.83[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10835185	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10835191	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11030054	0.96[ASN][1000 genomes]
rs12278324	0.85[ASN][1000 genomes]
rs12417801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12421093	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12795081	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3813879	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3813880	0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910858	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7131058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1046325	chr11:3856201-3895148	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv1039059	chr11:3856201-3909415	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
10	nsv540910	chr11:3856201-3909415	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1051580	chr11:3856201-3924216	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
12	nsv1043265	chr11:3856201-3926407	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
13	nsv896894	chr11:3859856-3888234	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1869002	IFITM3	cis	cerebellum	SCAN
rs1869002	PGAP2	cis	brain	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3863000-3874600	Weak transcription	Psoas Muscle	Psoas
2	chr11:3863000-3875400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:3863400-3873600	Weak transcription	Thymus	Thymus
4	chr11:3863600-3870600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr11:3863600-3875200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:3864000-3872800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr11:3864600-3870600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr11:3867000-3875600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr11:3867200-3873800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:3867400-3874000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr11:3867600-3873800	Weak transcription	Fetal Thymus	thymus
12	chr11:3869400-3871000	Enhancers	HepG2	liver
13	chr11:3869600-3871000	Enhancers	Liver	Liver
14	chr11:3869600-3871000	Enhancers	K562	blood
15	chr11:3869800-3870600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:3870200-3870600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr11:3870200-3870600	Enhancers	Dnd41	blood
18	chr11:3870200-3871000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:3870200-3871000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr11:3870200-3871000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr11:3870200-3871000	Enhancers	A549	lung
22	chr11:3870400-3870800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr11:3870400-3870800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr11:3870400-3871000	Enhancers	Primary B cells from peripheral blood	blood
25	chr11:3870400-3871000	Enhancers	Primary T cells from cord blood	blood
26	chr11:3870400-3871000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr11:3870400-3871000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr11:3870400-3871000	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links