Variant report

Variant	rs11676884
Chromosome Location	chr2:30466066-30466067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30465310..30467321-chr2:30469848..30471396,2	MCF-7	breast:
2	chr2:30463829..30466143-chr2:30472791..30475972,4	K562	blood:
3	chr2:30455825..30457692-chr2:30465577..30467870,2	MCF-7	breast:
4	chr2:30465899..30468509-chr2:30882716..30885823,3	K562	blood:

Variant related genes	Relation type
ENSG00000213626	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1001204	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11678385	0.81[CEU][hapmap]
rs13386455	0.93[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs13389106	0.91[ASN][1000 genomes]
rs17009304	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs17321999	0.93[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1962588	0.92[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs2089657	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2362541	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3813658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4384829	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4564821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4952115	0.93[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs57667995	0.83[EUR][1000 genomes]
rs58645306	0.96[ASN][1000 genomes]
rs59693338	0.96[ASN][1000 genomes]
rs6548005	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs6708792	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs6732241	0.93[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6736034	0.94[ASW][hapmap];0.80[GIH][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs72787716	0.95[ASN][1000 genomes]
rs72787718	0.96[ASN][1000 genomes]
rs72787719	0.95[ASN][1000 genomes]
rs73925103	0.95[ASN][1000 genomes]
rs906865	0.93[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs906866	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs906867	0.93[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9798481	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][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	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1002657	chr2:30339312-30516535	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv2662	chr2:30462905-30495134	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11676884	IFT172	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30457000-30476600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:30457200-30470400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:30457200-30473000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:30457400-30466400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:30457600-30471800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:30457800-30467400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:30457800-30481000	Weak transcription	Gastric	stomach
8	chr2:30458400-30475800	Weak transcription	Fetal Kidney	kidney
9	chr2:30460800-30471800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:30461000-30479800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:30461400-30469400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
12	chr2:30461800-30472200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:30462200-30473200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:30462400-30468200	Weak transcription	GM12878-XiMat	blood
15	chr2:30462600-30468200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:30462600-30468200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:30462800-30466600	Strong transcription	NH-A	brain
18	chr2:30462800-30471200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:30462800-30474800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:30462800-30475400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr2:30463000-30467400	Genic enhancers	A549	lung
22	chr2:30463000-30471000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:30463000-30473000	Weak transcription	Fetal Intestine Small	intestine
24	chr2:30463000-30474200	Weak transcription	Fetal Intestine Large	intestine
25	chr2:30463000-30474800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:30463000-30475400	Genic enhancers	Primary T cells fromperipheralblood	blood
27	chr2:30463200-30466200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:30463200-30466800	Weak transcription	Fetal Brain Female	brain
29	chr2:30463200-30471200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:30463400-30466200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:30463400-30467000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr2:30463400-30472400	Strong transcription	HSMM	muscle
33	chr2:30463400-30473400	Weak transcription	Ovary	ovary
34	chr2:30463400-30474800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:30463400-30474800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:30463400-30475000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:30463400-30475400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:30463400-30475600	Weak transcription	Brain Germinal Matrix	brain
39	chr2:30463400-30475600	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:30463400-30475600	Weak transcription	Esophagus	oesophagus
41	chr2:30463600-30466400	Weak transcription	Fetal Stomach	stomach
42	chr2:30463600-30468400	Weak transcription	Spleen	Spleen
43	chr2:30463600-30472200	Weak transcription	Lung	lung
44	chr2:30463600-30472200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:30463600-30472400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:30463600-30473200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:30463600-30475600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:30463600-30475600	Weak transcription	Osteobl	bone
49	chr2:30463800-30466800	Weak transcription	Dnd41	blood
50	chr2:30463800-30470400	Weak transcription	Fetal Muscle Leg	muscle

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