Variant report

Variant	rs2248655
Chromosome Location	chr11:93254612-93254613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:93253490..93255254-chr11:93255715..93258360,2	K562	blood:

Variant related genes	Relation type
ENSG00000166002	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10466368	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11601056	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11604909	0.83[EUR][1000 genomes]
rs1563445	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2243410	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248020	0.96[EUR][1000 genomes]
rs2248524	0.93[EUR][1000 genomes]
rs2248531	0.93[EUR][1000 genomes]
rs2605611	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2605614	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2605615	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2605617	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2605620	0.93[EUR][1000 genomes]
rs2605622	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605623	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605626	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605627	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2605628	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2605629	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2658766	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2658768	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2658769	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2658770	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7116173	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
rs2248655	CCDC67	cis	Thyroid	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93226400-93257400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr11:93227200-93257600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:93233000-93257400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr11:93235400-93257800	Weak transcription	Gastric	stomach
5	chr11:93235600-93258800	Weak transcription	Small Intestine	intestine
6	chr11:93238400-93259000	Weak transcription	Fetal Lung	lung
7	chr11:93239600-93255600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:93241800-93257400	Weak transcription	Fetal Intestine Large	intestine
9	chr11:93243800-93255600	Weak transcription	Fetal Intestine Small	intestine
10	chr11:93248000-93261800	Weak transcription	Fetal Stomach	stomach
11	chr11:93248800-93257400	Weak transcription	Adipose Nuclei	Adipose
12	chr11:93249000-93261600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr11:93249200-93255400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:93249200-93255600	Weak transcription	Left Ventricle	heart
15	chr11:93249200-93255600	Weak transcription	Right Ventricle	heart
16	chr11:93249200-93257600	Weak transcription	Fetal Muscle Leg	muscle
17	chr11:93249200-93257600	Weak transcription	Placenta	Placenta
18	chr11:93249200-93257800	Weak transcription	Right Atrium	heart
19	chr11:93250600-93255400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr11:93250800-93255400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:93251000-93258200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:93251000-93261400	Weak transcription	Fetal Brain Male	brain
23	chr11:93251000-93261600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr11:93251000-93261600	Weak transcription	Aorta	Aorta
25	chr11:93251200-93255400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr11:93251200-93255400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:93251800-93255000	Enhancers	Thymus	Thymus
28	chr11:93252000-93257000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:93252000-93266800	Enhancers	Fetal Thymus	thymus
30	chr11:93252200-93257000	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr11:93252200-93259000	Enhancers	Liver	Liver
32	chr11:93252200-93260800	Enhancers	Dnd41	blood
33	chr11:93252400-93257000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr11:93252600-93259800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr11:93253000-93255400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:93253000-93257200	Weak transcription	HSMMtube	muscle
37	chr11:93253000-93258800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr11:93253200-93256400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr11:93253400-93255000	Enhancers	Primary T cells from cord blood	blood
40	chr11:93253400-93257600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr11:93253400-93257600	Weak transcription	Stomach Mucosa	stomach
42	chr11:93253600-93255000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:93253600-93255200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr11:93253600-93256000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr11:93253600-93256800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr11:93253800-93255200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:93253800-93255600	Enhancers	Primary hematopoietic stem cells	blood
48	chr11:93253800-93266200	Weak transcription	Fetal Brain Female	brain
49	chr11:93254000-93254800	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr11:93254000-93254800	Flanking Active TSS	GM12878-XiMat	blood

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