Variant report

Variant	rs2466369
Chromosome Location	chr3:101457391-101457392
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13090844	0.80[EUR][1000 genomes]
rs2449492	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2449493	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2611836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2611840	1.00[ASN][1000 genomes]
rs2625282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2625283	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2625289	0.95[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2722162	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2722166	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665631	1.00[MEX][hapmap]
rs6764700	0.93[TSI][hapmap];1.00[YRI][hapmap]
rs6774950	0.82[YRI][hapmap]
rs6794860	1.00[ASW][hapmap];0.93[TSI][hapmap]
rs6805496	0.92[TSI][hapmap]
rs6806256	0.93[TSI][hapmap];0.81[AMR][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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2466369	FAM55C	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101445600-101497400	Weak transcription	Fetal Heart	heart
2	chr3:101451400-101459600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:101451600-101463400	Weak transcription	HepG2	liver
4	chr3:101451800-101476600	Weak transcription	Psoas Muscle	Psoas
5	chr3:101452800-101457600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:101453000-101458200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:101453400-101478400	Weak transcription	Small Intestine	intestine
8	chr3:101453800-101473600	Weak transcription	HSMMtube	muscle
9	chr3:101453800-101474200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:101453800-101487000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr3:101454000-101457400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:101454000-101458200	Weak transcription	NHDF-Ad	bronchial
13	chr3:101454000-101474000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:101454200-101458600	Weak transcription	NH-A	brain
15	chr3:101454200-101473000	Weak transcription	HSMM	muscle
16	chr3:101454200-101474200	Weak transcription	HMEC	breast
17	chr3:101454400-101464400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:101454600-101463800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:101454600-101473400	Weak transcription	Hela-S3	cervix
20	chr3:101454600-101476400	Weak transcription	NHEK	skin
21	chr3:101454600-101476600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:101454800-101474200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:101454800-101476600	Weak transcription	A549	lung
24	chr3:101455000-101463600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:101455200-101457400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:101455200-101476600	Weak transcription	Pancreas	Pancrea
27	chr3:101455400-101457800	Weak transcription	Fetal Stomach	stomach
28	chr3:101455400-101463800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:101455400-101473000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:101455400-101473000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:101455400-101473400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:101455400-101473400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:101455400-101474200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:101455400-101474200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:101455400-101474200	Weak transcription	Aorta	Aorta
36	chr3:101455400-101474200	Weak transcription	Brain Angular Gyrus	brain
37	chr3:101455400-101474200	Weak transcription	Brain Substantia Nigra	brain
38	chr3:101455400-101474200	Weak transcription	Colonic Mucosa	Colon
39	chr3:101455400-101474200	Weak transcription	Esophagus	oesophagus
40	chr3:101455400-101474200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:101455400-101474400	Weak transcription	Ovary	ovary
42	chr3:101455400-101474400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:101455400-101474600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:101455400-101476200	Weak transcription	NHLF	lung
45	chr3:101455400-101476600	Weak transcription	Right Ventricle	heart
46	chr3:101455400-101476600	Weak transcription	K562	blood
47	chr3:101455400-101477800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:101455600-101458400	Weak transcription	Fetal Intestine Large	intestine
49	chr3:101455600-101458400	Weak transcription	Gastric	stomach
50	chr3:101455600-101458600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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