Variant report

Variant	rs11604909
Chromosome Location	chr11:93218355-93218356
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10466368	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11601056	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1563445	0.86[CEU][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs2248020	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs2248524	0.81[CEU][hapmap]
rs2248655	0.83[EUR][1000 genomes]
rs2446061	0.85[CEU][hapmap]
rs2605581	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs2605583	0.85[CEU][hapmap]
rs2605611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2605614	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2605615	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2605617	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2605626	0.86[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.84[EUR][1000 genomes]
rs2605627	0.82[EUR][1000 genomes]
rs2605629	0.81[CEU][hapmap];0.86[MEX][hapmap]
rs2608214	0.95[GIH][hapmap]
rs2658766	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2658768	0.83[EUR][1000 genomes]
rs2658769	0.84[EUR][1000 genomes]
rs2658770	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs2658777	0.85[CEU][hapmap]
rs2658778	0.85[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs2658779	0.85[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs2658781	0.85[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs2658791	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2925355	0.95[GIH][hapmap]
rs3133443	0.83[AMR][1000 genomes]
rs7116173	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72972357	0.82[EUR][1000 genomes]
rs72972364	0.82[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	nsv1039134	chr11:92790000-93219942	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv1039623	chr11:93141461-93328739	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	esv2760208	chr11:93172673-93266594	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11604909	CCDC67	cis	Thyroid	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93207000-93239000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:93207800-93220000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:93208200-93223200	Weak transcription	GM12878-XiMat	blood
4	chr11:93208400-93218400	Weak transcription	Left Ventricle	heart
5	chr11:93209000-93231400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:93209000-93235200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr11:93209200-93229200	Weak transcription	Dnd41	blood
8	chr11:93209400-93218800	Strong transcription	Fetal Intestine Small	intestine
9	chr11:93209600-93229400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr11:93210600-93220000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr11:93210600-93231600	Weak transcription	A549	lung
12	chr11:93211000-93218600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr11:93211000-93225800	Weak transcription	Thymus	Thymus
14	chr11:93211000-93253400	Weak transcription	Primary T cells from cord blood	blood
15	chr11:93211200-93222000	Weak transcription	Adipose Nuclei	Adipose
16	chr11:93211600-93219000	Weak transcription	HepG2	liver
17	chr11:93211600-93220400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr11:93211600-93223000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr11:93211600-93243800	Weak transcription	Fetal Thymus	thymus
20	chr11:93211800-93218600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:93211800-93220200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr11:93212000-93220000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr11:93212200-93220600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:93212200-93221200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr11:93212200-93222800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr11:93212200-93234800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:93212400-93222600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr11:93212400-93225800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr11:93213000-93219200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:93213000-93220400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr11:93213000-93221200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr11:93213000-93221400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr11:93213400-93218800	Enhancers	Fetal Brain Male	brain
34	chr11:93214400-93221200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr11:93214800-93220200	Weak transcription	Aorta	Aorta
36	chr11:93214800-93234400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr11:93215200-93218400	Weak transcription	Esophagus	oesophagus
38	chr11:93215200-93220800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:93215200-93221800	Weak transcription	Gastric	stomach
40	chr11:93215200-93225400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr11:93215400-93222600	Enhancers	Fetal Lung	lung
42	chr11:93215600-93218400	Weak transcription	Lung	lung
43	chr11:93215600-93218800	Enhancers	Fetal Brain Female	brain
44	chr11:93215600-93225800	Weak transcription	Colonic Mucosa	Colon
45	chr11:93215600-93226000	Weak transcription	Stomach Mucosa	stomach
46	chr11:93215800-93220200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr11:93216000-93219600	Weak transcription	Right Atrium	heart
48	chr11:93216000-93219800	Enhancers	Fetal Muscle Trunk	muscle
49	chr11:93216000-93221800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr11:93216000-93224600	Weak transcription	Rectal Mucosa Donor 29	rectum

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