Variant report

Variant	rs2727487
Chromosome Location	chr7:129513820-129513821
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:129497829..129499402-chr7:129513629..129516363,2	K562	blood:
2	chr7:129501152..129503264-chr7:129513398..129515924,2	K562	blood:
3	chr7:129472642..129475029-chr7:129512256..129514078,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186591	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10215972	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11765073	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1464973	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1471875	0.85[AFR][1000 genomes]
rs1471876	0.81[LWK][hapmap]
rs1725077	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1725078	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2402980	0.80[AFR][1000 genomes]
rs2631602	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs2631603	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2631611	0.86[EUR][1000 genomes]
rs2693724	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2693725	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708637	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708649	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2727462	0.98[ASN][1000 genomes]
rs2727464	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]
rs2727477	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2727483	0.97[ASN][1000 genomes]
rs2727488	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2727489	0.88[ASN][1000 genomes]
rs2727490	1.00[ASN][1000 genomes]
rs2727492	0.96[ASN][1000 genomes]
rs2727499	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2727500	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2727502	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2727507	0.87[LWK][hapmap];1.00[YRI][hapmap]
rs3807120	0.93[JPT][hapmap]
rs3817530	0.86[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2727487	SMO	cis	cerebellum	SCAN
rs2727487	C7orf45	cis	cerebellum	SCAN
rs2727487	LOC407835	cis	parietal	SCAN
rs2727487	FSCN3	cis	cerebellum	SCAN

Chromatin state (count:120 , 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	chr7:129494400-129518800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr7:129495600-129517000	Weak transcription	Fetal Lung	lung
5	chr7:129496400-129520400	Weak transcription	Fetal Brain Female	brain
6	chr7:129497000-129515800	Weak transcription	Placenta	Placenta
7	chr7:129497000-129536800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:129499200-129517200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr7:129503000-129517200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:129503200-129515600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:129503200-129515800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr7:129503200-129517000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:129503200-129517200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr7:129503200-129519800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr7:129503200-129529000	Weak transcription	Gastric	stomach
16	chr7:129503400-129514400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr7:129503400-129515800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr7:129503400-129517200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr7:129503400-129538400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:129503600-129515600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr7:129503600-129515800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr7:129503800-129515400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:129504000-129517800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr7:129504000-129518800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr7:129504200-129515600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr7:129504200-129515600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr7:129504200-129515600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr7:129504200-129517200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr7:129504200-129519200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr7:129504600-129518000	Weak transcription	Lung	lung
31	chr7:129505600-129529600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr7:129505600-129545600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr7:129506000-129515000	Weak transcription	NHLF	lung
34	chr7:129506000-129515600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr7:129506000-129518000	Weak transcription	Pancreas	Pancrea
36	chr7:129506000-129518000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr7:129506000-129542800	Weak transcription	Small Intestine	intestine
38	chr7:129506400-129514600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr7:129506400-129516600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr7:129506400-129517000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr7:129506600-129514600	Weak transcription	A549	lung
42	chr7:129506600-129515600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr7:129506600-129515800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr7:129506600-129515800	Weak transcription	Stomach Mucosa	stomach
45	chr7:129506600-129517400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr7:129506800-129514800	Weak transcription	NHDF-Ad	bronchial
47	chr7:129506800-129515000	Weak transcription	NH-A	brain
48	chr7:129506800-129515400	Weak transcription	Hela-S3	cervix
49	chr7:129506800-129515600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr7:129506800-129515600	Weak transcription	Brain Anterior Caudate	brain

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