Variant report

Variant	rs2727500
Chromosome Location	chr7:129475323-129475324
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:129473601..129475464-chr7:129483502..129485104,2	MCF-7	breast:
2	chr7:129474246..129476475-chr7:129476577..129479006,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10215972	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11765073	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1464973	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1471875	0.83[AFR][1000 genomes]
rs1471876	0.85[LWK][hapmap]
rs1725077	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1725078	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2402980	0.90[AFR][1000 genomes]
rs2631602	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs2631603	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2631611	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2693724	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2693725	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2708637	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708649	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2727462	1.00[ASN][1000 genomes]
rs2727464	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]
rs2727477	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2727482	0.89[AFR][1000 genomes]
rs2727483	0.94[ASN][1000 genomes]
rs2727487	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]
rs2727488	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2727489	0.86[ASN][1000 genomes]
rs2727490	0.98[ASN][1000 genomes]
rs2727492	0.97[ASN][1000 genomes]
rs2727499	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2727502	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2727507	0.91[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2727500	FSCN3	cis	cerebellum	SCAN
rs2727500	SMO	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129466200-129483800	Weak transcription	Dnd41	blood
2	chr7:129466400-129483400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr7:129470000-129480400	Weak transcription	Fetal Brain Male	brain
4	chr7:129470400-129480200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:129470400-129480400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:129470400-129480600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr7:129470400-129480800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:129470400-129480800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr7:129470400-129483600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr7:129470600-129480400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:129470600-129480600	Weak transcription	Brain Angular Gyrus	brain
12	chr7:129470800-129479000	Strong transcription	Fetal Intestine Small	intestine
13	chr7:129470800-129480200	Weak transcription	Brain Germinal Matrix	brain
14	chr7:129471200-129479200	Strong transcription	Fetal Stomach	stomach
15	chr7:129471200-129479800	Strong transcription	Primary T cells from cord blood	blood
16	chr7:129471400-129475400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:129471600-129477200	Strong transcription	Thymus	Thymus
18	chr7:129471600-129479000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr7:129471600-129479200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr7:129471600-129479200	Strong transcription	Liver	Liver
21	chr7:129471600-129479400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr7:129471600-129479400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr7:129471600-129479400	Strong transcription	Fetal Thymus	thymus
24	chr7:129471600-129480600	Weak transcription	Brain Substantia Nigra	brain
25	chr7:129471800-129478000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr7:129472000-129479600	Strong transcription	Primary B cells from cord blood	blood
27	chr7:129472200-129479200	Strong transcription	Fetal Intestine Large	intestine
28	chr7:129472200-129479200	Strong transcription	Fetal Muscle Leg	muscle
29	chr7:129472200-129484200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr7:129472400-129476200	Weak transcription	Spleen	Spleen
31	chr7:129472400-129476800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:129472400-129476800	Weak transcription	Aorta	Aorta
33	chr7:129472400-129479400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:129472400-129480200	Weak transcription	Psoas Muscle	Psoas
35	chr7:129472600-129480200	Weak transcription	Pancreas	Pancrea
36	chr7:129472600-129480400	Weak transcription	Right Atrium	heart
37	chr7:129472600-129480800	Weak transcription	A549	lung
38	chr7:129472800-129475600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:129472800-129478200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr7:129472800-129491400	Weak transcription	Fetal Kidney	kidney
41	chr7:129473000-129475400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr7:129473000-129475600	Strong transcription	HUVEC	blood vessel
43	chr7:129473000-129476200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:129473000-129477000	Weak transcription	HSMM	muscle
45	chr7:129473000-129477800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr7:129473000-129479200	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr7:129473200-129475600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:129473200-129475600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr7:129473200-129476200	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr7:129473200-129479200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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