Variant report

Variant	rs4564821
Chromosome Location	chr2:30474255-30474256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30452787..30458792-chr2:30474216..30479125,11	K562	blood:
2	chr2:30463829..30466143-chr2:30472791..30475972,4	K562	blood:
3	chr2:30459999..30464804-chr2:30474137..30477672,6	K562	blood:
4	chr2:30457858..30460277-chr2:30473755..30476331,2	K562	blood:

Variant related genes	Relation type
ENSG00000213626	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1001204	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11676884	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]
rs11678385	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs13386455	0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13389106	0.94[ASN][1000 genomes]
rs17009304	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17321999	0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1962588	0.92[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2089657	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2362541	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3813658	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4384829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4952115	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs57667995	0.86[EUR][1000 genomes]
rs58645306	0.99[ASN][1000 genomes]
rs59693338	0.97[ASN][1000 genomes]
rs6548005	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6708792	1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs6732241	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6736034	0.83[GIH][hapmap];0.80[MKK][hapmap]
rs72787716	0.96[ASN][1000 genomes]
rs72787718	0.99[ASN][1000 genomes]
rs72787719	0.98[ASN][1000 genomes]
rs73925103	0.98[ASN][1000 genomes]
rs906865	0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs906866	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs906867	0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9798481	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4564821	LBH	cis	cerebellum	SCAN
rs4564821	IFT172	cis	cerebellum	SCAN

Chromatin state (count:95 , 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	chr2:30457800-30481000	Weak transcription	Gastric	stomach
3	chr2:30458400-30475800	Weak transcription	Fetal Kidney	kidney
4	chr2:30461000-30479800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:30462800-30474800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:30462800-30475400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr2:30463000-30474800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:30463000-30475400	Genic enhancers	Primary T cells fromperipheralblood	blood
9	chr2:30463400-30474800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:30463400-30474800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:30463400-30475000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:30463400-30475400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:30463400-30475600	Weak transcription	Brain Germinal Matrix	brain
14	chr2:30463400-30475600	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:30463400-30475600	Weak transcription	Esophagus	oesophagus
16	chr2:30463600-30475600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:30463600-30475600	Weak transcription	Osteobl	bone
18	chr2:30463800-30474800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:30464200-30474600	Weak transcription	Small Intestine	intestine
20	chr2:30465400-30480000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:30466000-30477000	Genic enhancers	Primary B cells from peripheral blood	blood
22	chr2:30466200-30476400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
23	chr2:30466200-30480400	Weak transcription	Fetal Brain Male	brain
24	chr2:30466600-30474600	Weak transcription	NH-A	brain
25	chr2:30467200-30475600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:30467400-30475600	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr2:30467600-30479600	Weak transcription	Fetal Brain Female	brain
28	chr2:30468000-30475400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:30468600-30475600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:30469800-30475000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr2:30470200-30474400	Genic enhancers	NHLF	lung
32	chr2:30470400-30474800	Enhancers	K562	blood
33	chr2:30470400-30478000	Enhancers	Left Ventricle	heart
34	chr2:30470400-30479600	Genic enhancers	Fetal Thymus	thymus
35	chr2:30470600-30475000	Genic enhancers	A549	lung
36	chr2:30470800-30475200	Genic enhancers	Thymus	Thymus
37	chr2:30471000-30484400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:30471200-30479600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr2:30471200-30482000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:30471400-30479400	Enhancers	Placenta	Placenta
41	chr2:30471600-30474800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:30471800-30481600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:30472000-30475000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
44	chr2:30472200-30474400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:30472200-30474400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr2:30472200-30475000	Genic enhancers	Spleen	Spleen
47	chr2:30472200-30475600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:30472200-30476200	Enhancers	Lung	lung
49	chr2:30472200-30478800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:30472200-30480400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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