Variant report

Variant	rs2276102
Chromosome Location	chr11:87013438-87013439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10751151	0.82[ASN][1000 genomes]
rs10751152	0.82[ASN][1000 genomes]
rs10751153	0.83[ASN][1000 genomes]
rs10792935	0.83[ASN][1000 genomes]
rs10792937	0.83[ASN][1000 genomes]
rs10792938	0.83[ASN][1000 genomes]
rs10792940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898663	0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10898665	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11235083	0.83[ASN][1000 genomes]
rs12272741	0.83[ASN][1000 genomes]
rs12273325	0.82[ASN][1000 genomes]
rs12288478	0.82[ASN][1000 genomes]
rs1893004	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1893005	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1893229	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4400838	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4545589	0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap]
rs4944697	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6592346	0.82[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6592347	0.81[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6592349	0.80[ASN][1000 genomes]
rs6592352	0.83[ASN][1000 genomes]
rs6592355	0.83[ASN][1000 genomes]
rs7108829	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7118558	0.83[ASN][1000 genomes]
rs7931059	0.82[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7947510	0.82[ASN][1000 genomes]
rs9666962	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]

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	nsv1043562	chr11:86755535-87547185	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv541120	chr11:86755535-87547185	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1046288	chr11:86757573-87158571	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1045057	chr11:86794670-87033779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv541121	chr11:86794670-87033779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv898064	chr11:86864277-87013438	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2829956	chr11:86872504-87025059	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv898073	chr11:86963330-87013438	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
9	nsv898074	chr11:86963330-87034696	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	n/a
10	nsv555713	chr11:86971548-87013438	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2276102	CCDC89	cis	cerebellum	SCAN
rs2276102	AZU1	trans	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86991600-87014200	Weak transcription	HepG2	liver
2	chr11:86992000-87017600	Weak transcription	Aorta	Aorta
3	chr11:86992600-87020600	Weak transcription	Liver	Liver
4	chr11:86994000-87014200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:86995200-87018800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:87004000-87032600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:87006400-87030600	Weak transcription	Dnd41	blood
8	chr11:87008400-87017400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:87010200-87017400	Weak transcription	Small Intestine	intestine
10	chr11:87010200-87037200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr11:87010600-87018000	Weak transcription	Gastric	stomach
12	chr11:87010600-87036800	Weak transcription	Psoas Muscle	Psoas
13	chr11:87010800-87017400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr11:87011600-87013800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:87011800-87013800	Enhancers	Brain Substantia Nigra	brain
16	chr11:87011800-87024000	Weak transcription	Fetal Brain Female	brain
17	chr11:87011800-87036800	Weak transcription	Primary B cells from cord blood	blood
18	chr11:87012000-87013800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr11:87012000-87014200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr11:87012000-87014200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr11:87012000-87014800	Weak transcription	Fetal Kidney	kidney
22	chr11:87012000-87017400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:87012000-87017400	Weak transcription	Ovary	ovary
24	chr11:87012000-87024600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr11:87012000-87032200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr11:87012000-87034200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr11:87012000-87040400	Weak transcription	Fetal Intestine Small	intestine
28	chr11:87012200-87014200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr11:87012200-87018000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr11:87012200-87020400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:87012400-87013800	Enhancers	HUVEC	blood vessel
32	chr11:87012400-87017600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr11:87012400-87030400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr11:87012400-87032200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr11:87012600-87015200	Weak transcription	Left Ventricle	heart
36	chr11:87012600-87017400	Weak transcription	Adipose Nuclei	Adipose
37	chr11:87012600-87017400	Weak transcription	Fetal Thymus	thymus
38	chr11:87012600-87017400	Weak transcription	Spleen	Spleen
39	chr11:87012600-87017400	Weak transcription	K562	blood
40	chr11:87012600-87017600	Weak transcription	Right Atrium	heart
41	chr11:87012600-87017600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr11:87012600-87017800	Weak transcription	Pancreas	Pancrea
43	chr11:87012600-87019200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:87012600-87019400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr11:87012600-87030200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:87012600-87031000	Weak transcription	Primary T cells from cord blood	blood
47	chr11:87012600-87032200	Weak transcription	Brain Anterior Caudate	brain
48	chr11:87012600-87032200	Weak transcription	Fetal Intestine Large	intestine
49	chr11:87012600-87036000	Weak transcription	Fetal Muscle Leg	muscle
50	chr11:87012600-87036400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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