Variant report

Variant	rs2362541
Chromosome Location	chr2:30478453-30478454
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:30475522-30479423	A549	lung:	n/a	n/a
2	POLR2A	chr2:30478290-30478578	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr2:30477119-30482747	SK-N-MC	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:30452787..30458792-chr2:30474216..30479125,11	K562	blood:
2	chr2:30475603..30478549-chr2:30478723..30480577,2	K562	blood:
3	chr2:30451092..30457677-chr2:30474497..30480716,15	K562	blood:
4	chr2:30475438..30481096-chr2:30481124..30485591,9	K562	blood:
5	chr2:30469843..30471764-chr2:30477374..30479207,2	MCF-7	breast:
6	chr2:30475984..30481096-chr2:30481124..30486276,10	K562	blood:
7	chr2:30476489..30478735-chr2:30510499..30512254,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000256261	TF binding region
ENSG00000256261	Chromatin interaction
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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11676884	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]
rs11678385	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs13386455	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13389106	0.96[ASN][1000 genomes]
rs17009304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17321999	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1962588	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2089657	0.93[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs3813658	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4384829	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4564821	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]
rs4952115	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs57667995	0.87[EUR][1000 genomes]
rs58645306	0.97[ASN][1000 genomes]
rs59693338	0.95[ASN][1000 genomes]
rs6548005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6708792	0.92[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs6732241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6736034	0.88[ASW][hapmap];0.92[YRI][hapmap]
rs72787716	0.94[ASN][1000 genomes]
rs72787718	0.97[ASN][1000 genomes]
rs72787719	0.96[ASN][1000 genomes]
rs73925103	0.96[ASN][1000 genomes]
rs906865	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs906866	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs906867	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9798481	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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
rs2362541	LBH	cis	cerebellum	SCAN
rs2362541	IFT172	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30457800-30481000	Weak transcription	Gastric	stomach
2	chr2:30461000-30479800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:30465400-30480000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:30466200-30480400	Weak transcription	Fetal Brain Male	brain
5	chr2:30467600-30479600	Weak transcription	Fetal Brain Female	brain
6	chr2:30470400-30479600	Genic enhancers	Fetal Thymus	thymus
7	chr2:30471000-30484400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:30471200-30479600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:30471200-30482000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:30471400-30479400	Enhancers	Placenta	Placenta
11	chr2:30471800-30481600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:30472200-30478800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:30472200-30480400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr2:30472600-30480000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:30472600-30483400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:30473000-30479600	Enhancers	Fetal Heart	heart
17	chr2:30473200-30480000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr2:30473400-30480800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr2:30473400-30480800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:30474200-30479400	Enhancers	Fetal Intestine Large	intestine
21	chr2:30474200-30480800	Enhancers	Pancreas	Pancrea
22	chr2:30474400-30481400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:30475600-30478600	Enhancers	Fetal Muscle Leg	muscle
24	chr2:30476000-30479000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:30476000-30480200	Weak transcription	GM12878-XiMat	blood
26	chr2:30476200-30479400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr2:30476200-30479400	Genic enhancers	HSMM	muscle
28	chr2:30476200-30479600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr2:30476200-30479800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:30476200-30480000	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr2:30476200-30480200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:30476200-30481200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:30476200-30481400	Weak transcription	Esophagus	oesophagus
34	chr2:30476200-30483400	Weak transcription	Brain Anterior Caudate	brain
35	chr2:30476400-30481400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:30476600-30478600	Genic enhancers	A549	lung
37	chr2:30476600-30479200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:30476600-30481400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:30476600-30496000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:30476800-30478600	Strong transcription	Primary B cells from cord blood	blood
41	chr2:30476800-30478800	Genic enhancers	NHLF	lung
42	chr2:30476800-30479000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:30476800-30479000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:30476800-30479400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:30476800-30479400	Weak transcription	Osteobl	bone
46	chr2:30476800-30479800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr2:30476800-30480000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr2:30476800-30480400	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:30476800-30480400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr2:30476800-30480600	Weak transcription	Colonic Mucosa	Colon

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