Variant report

Variant	rs7129444
Chromosome Location	chr11:3933032-3933033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10500590	0.91[GIH][hapmap]
rs10742189	0.82[ASW][hapmap];0.81[GIH][hapmap]
rs10767715	0.91[GIH][hapmap]
rs10767767	0.93[GIH][hapmap]
rs10767811	0.87[GIH][hapmap]
rs10835290	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835340	0.91[GIH][hapmap]
rs10835403	0.91[GIH][hapmap]
rs10835407	0.91[GIH][hapmap]
rs10835596	0.87[GIH][hapmap]
rs11030404	0.82[GIH][hapmap]
rs11030639	0.93[GIH][hapmap]
rs11030781	0.87[GIH][hapmap]
rs11030918	0.80[GIH][hapmap]
rs12286851	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1349583	0.91[GIH][hapmap]
rs1452047	0.91[GIH][hapmap]
rs17081	0.91[GIH][hapmap]
rs17279635	0.91[GIH][hapmap]
rs2923948	0.83[GIH][hapmap]
rs4910869	0.91[GIH][hapmap]
rs7924984	0.82[GIH][hapmap]
rs7950153	0.89[GIH][hapmap]
rs963998	0.87[GIH][hapmap]
rs995498	0.91[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
6	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
7	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv1051904	chr11:3903226-3939186	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv1050077	chr11:3903226-3940726	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv1043039	chr11:3903226-3955159	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7129444	IFITM3	cis	parietal	SCAN
rs7129444	KCNQ1	cis	parietal	SCAN
rs7129444	RRM1	cis	Nerve Tibial	GTEx
rs7129444	RASSF7	cis	parietal	SCAN
rs7129444	OR51A4	cis	parietal	SCAN
rs7129444	RRM1	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3916600-3943800	Weak transcription	Fetal Stomach	stomach
2	chr11:3916600-3948800	Weak transcription	Aorta	Aorta
3	chr11:3924000-3950600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:3924200-3934400	Weak transcription	Gastric	stomach
5	chr11:3924800-3938200	Weak transcription	Pancreas	Pancrea
6	chr11:3925800-3941000	Weak transcription	Right Ventricle	heart
7	chr11:3926600-3938400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr11:3926600-3941000	Weak transcription	Small Intestine	intestine
9	chr11:3926800-3937000	Weak transcription	Lung	lung
10	chr11:3927200-3933200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:3927200-3936000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:3927200-3942600	Weak transcription	Spleen	Spleen
13	chr11:3927400-3941200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr11:3927600-3943600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr11:3928400-3940800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:3928800-3938200	Weak transcription	A549	lung
17	chr11:3929000-3938200	Weak transcription	Esophagus	oesophagus
18	chr11:3929200-3934200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:3929200-3934400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:3929200-3935400	Weak transcription	Primary B cells from cord blood	blood
21	chr11:3929200-3935600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr11:3929200-3936000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:3929200-3937200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:3929200-3938200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr11:3929200-3940800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:3929400-3937200	Weak transcription	Dnd41	blood
27	chr11:3929400-3937400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:3929400-3938200	Weak transcription	GM12878-XiMat	blood
29	chr11:3929400-3950600	Weak transcription	Ovary	ovary
30	chr11:3930200-3938000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:3930400-3934600	Weak transcription	HepG2	liver
32	chr11:3930400-3936000	Weak transcription	HMEC	breast
33	chr11:3930400-3937000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:3930400-3937400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:3930600-3936000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr11:3930600-3938200	Weak transcription	Psoas Muscle	Psoas
37	chr11:3930600-3940800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr11:3931400-3933200	Enhancers	K562	blood
39	chr11:3931400-3934000	Weak transcription	Liver	Liver
40	chr11:3931400-3941000	Weak transcription	Adipose Nuclei	Adipose
41	chr11:3931600-3933200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr11:3931600-3942600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr11:3932000-3934400	Enhancers	Thymus	Thymus
44	chr11:3932000-3934800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr11:3932000-3935000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr11:3932200-3933400	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr11:3932200-3942800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr11:3932400-3933200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr11:3932400-3944000	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr11:3932600-3933200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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