Variant report

Variant	rs4243965
Chromosome Location	chr11:3886070-3886071
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11030210	1.00[ASW][hapmap];0.82[CEU][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs1823681	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2018918	1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs2920138	1.00[YRI][hapmap]
rs2923951	1.00[JPT][hapmap]
rs2959076	1.00[JPT][hapmap]
rs4243966	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910586	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7104206	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs7116483	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7118328	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
14	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4243965	CDKN1C	cis	cerebellum	SCAN
rs4243965	OR56A5	cis	cerebellum	SCAN
rs4243965	IFITM3	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3878200-3886800	Weak transcription	NHLF	lung
2	chr11:3879400-3886600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr11:3879400-3887200	Weak transcription	Fetal Brain Female	brain
4	chr11:3880600-3886800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:3881000-3886600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr11:3881000-3886800	Weak transcription	Brain Hippocampus Middle	brain
7	chr11:3881000-3888400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:3881200-3886200	Weak transcription	NHDF-Ad	bronchial
9	chr11:3881200-3886400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:3881200-3886400	Weak transcription	HSMMtube	muscle
11	chr11:3881200-3886600	Weak transcription	Colonic Mucosa	Colon
12	chr11:3881200-3886600	Weak transcription	Placenta	Placenta
13	chr11:3881200-3886600	Weak transcription	Right Atrium	heart
14	chr11:3881200-3886600	Weak transcription	HSMM	muscle
15	chr11:3881200-3886800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:3881200-3886800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:3881200-3886800	Weak transcription	Brain Substantia Nigra	brain
18	chr11:3881200-3886800	Weak transcription	Esophagus	oesophagus
19	chr11:3881200-3886800	Weak transcription	Gastric	stomach
20	chr11:3881200-3886800	Weak transcription	Pancreas	Pancrea
21	chr11:3881200-3887000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr11:3881200-3887000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:3881200-3888400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr11:3881200-3888600	Weak transcription	Ovary	ovary
25	chr11:3882000-3886600	Weak transcription	A549	lung
26	chr11:3882000-3886800	Weak transcription	NH-A	brain
27	chr11:3882200-3886400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr11:3882200-3888200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr11:3882400-3886400	Weak transcription	Stomach Mucosa	stomach
30	chr11:3882400-3886600	Weak transcription	Brain Angular Gyrus	brain
31	chr11:3882400-3886600	Weak transcription	Osteobl	bone
32	chr11:3882400-3886800	Weak transcription	Fetal Stomach	stomach
33	chr11:3882400-3886800	Enhancers	K562	blood
34	chr11:3882400-3887000	Weak transcription	Brain Germinal Matrix	brain
35	chr11:3882600-3889400	Enhancers	Primary T cells fromperipheralblood	blood
36	chr11:3882800-3886800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr11:3882800-3888800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr11:3883000-3886200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr11:3883000-3886600	Weak transcription	Brain Anterior Caudate	brain
40	chr11:3883000-3893200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr11:3883000-3893400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr11:3883200-3886600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:3883200-3886800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:3883200-3889400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:3883200-3890200	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr11:3883200-3893600	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr11:3883400-3886200	Weak transcription	HUVEC	blood vessel
48	chr11:3883400-3886600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:3883400-3887000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr11:3883400-3888600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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