Variant report

Variant	rs2727464
Chromosome Location	chr7:129502461-129502462
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:129502054-129502893	SK-N-SH	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:129250908..129252633-chr7:129501756..129504305,2	K562	blood:
2	chr7:129501152..129503264-chr7:129513398..129515924,2	K562	blood:
3	chr7:129500721..129502707-chr7:129502747..129505225,2	K562	blood:
4	chr7:129502118..129504872-chr7:129519208..129521665,2	MCF-7	breast:
5	chr7:129493067..129496024-chr7:129500943..129503078,3	K562	blood:
6	chr7:129493067..129496024-chr7:129500943..129503078,2	K562	blood:

No data

Variant related genes	Relation type
UBE2H	TF binding region
ENSG00000273329	Chromatin interaction
ENSG00000106459	Chromatin interaction
ENSG00000186591	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10215972	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs11765073	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1464973	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1471875	0.85[AFR][1000 genomes]
rs1471876	0.87[LWK][hapmap]
rs1725077	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1725078	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2402980	0.83[AFR][1000 genomes]
rs2631602	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs2631603	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2631611	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2693724	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2693725	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708637	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708649	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2727462	0.99[ASN][1000 genomes]
rs2727477	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2727482	0.82[AFR][1000 genomes]
rs2727483	0.94[ASN][1000 genomes]
rs2727487	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2727488	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2727489	0.85[ASN][1000 genomes]
rs2727490	0.97[ASN][1000 genomes]
rs2727492	0.96[ASN][1000 genomes]
rs2727499	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2727500	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2727502	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2727507	0.93[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs3807120	0.87[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533849	chr7:129462947-129616625	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2727464	SMO	cis	cerebellum	SCAN
rs2727464	FSCN3	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129475000-129534800	Weak transcription	Colonic Mucosa	Colon
2	chr7:129479400-129543600	Weak transcription	Thymus	Thymus
3	chr7:129481400-129510000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:129484200-129503000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:129485400-129503800	Weak transcription	Lung	lung
6	chr7:129486400-129505400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:129491600-129510000	Weak transcription	Fetal Intestine Large	intestine
8	chr7:129492000-129509200	Weak transcription	Fetal Intestine Small	intestine
9	chr7:129493800-129510400	Weak transcription	Brain Germinal Matrix	brain
10	chr7:129494400-129518800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr7:129495400-129510400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr7:129495600-129517000	Weak transcription	Fetal Lung	lung
13	chr7:129496200-129505600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr7:129496200-129509400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr7:129496400-129520400	Weak transcription	Fetal Brain Female	brain
16	chr7:129496800-129502600	Weak transcription	Fetal Stomach	stomach
17	chr7:129496800-129504000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:129496800-129509600	Weak transcription	HepG2	liver
19	chr7:129496800-129510200	Weak transcription	Fetal Thymus	thymus
20	chr7:129497000-129503200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr7:129497000-129503800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr7:129497000-129513400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr7:129497000-129515800	Weak transcription	Placenta	Placenta
24	chr7:129497000-129536800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr7:129497200-129511200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr7:129497400-129503000	Weak transcription	Hela-S3	cervix
27	chr7:129497800-129503000	Enhancers	Primary hematopoietic stem cells	blood
28	chr7:129497800-129505000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr7:129498000-129503800	Weak transcription	HSMM	muscle
30	chr7:129498200-129507200	Enhancers	Adipose Nuclei	Adipose
31	chr7:129498400-129503200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr7:129498400-129503600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr7:129498400-129506000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr7:129498600-129504400	Enhancers	K562	blood
35	chr7:129498600-129506800	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr7:129499200-129504800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr7:129499200-129517200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr7:129499400-129502800	Enhancers	Fetal Heart	heart
39	chr7:129499400-129502800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr7:129499400-129503000	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr7:129499400-129503400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr7:129499600-129506000	Enhancers	Pancreas	Pancrea
43	chr7:129499800-129502800	Enhancers	Stomach Smooth Muscle	stomach
44	chr7:129499800-129503000	Weak transcription	Osteobl	bone
45	chr7:129499800-129504200	Enhancers	GM12878-XiMat	blood
46	chr7:129499800-129509600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr7:129500000-129502600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr7:129500000-129503000	Weak transcription	NH-A	brain
49	chr7:129500000-129503200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr7:129500000-129503400	Enhancers	Primary neutrophils fromperipheralblood	blood

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