Variant report

Variant	rs4664103
Chromosome Location	chr2:153208713-153208714
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10432492	0.91[MEX][hapmap]
rs10931067	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10931068	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10931069	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11674872	0.91[MEX][hapmap]
rs12478426	0.91[MEX][hapmap]
rs13022419	0.80[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs13024533	0.82[EUR][1000 genomes]
rs13029771	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs13402243	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs13432002	0.86[CEU][hapmap];0.90[CHB][hapmap];0.97[EUR][1000 genomes]
rs16831028	0.80[MEX][hapmap]
rs2345873	0.82[CHD][hapmap];0.90[MEX][hapmap]
rs2345903	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28510143	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3890370	0.82[CHD][hapmap];0.90[MEX][hapmap]
rs4425036	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4547483	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4664106	0.80[MEX][hapmap]
rs4664569	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664570	0.86[ASN][1000 genomes]
rs4664573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58092541	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62179530	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62179556	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62180761	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62180766	0.81[EUR][1000 genomes]
rs6433984	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6704965	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6715843	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs6725656	1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6725789	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6754501	1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6757219	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9288090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	esv3693434	chr2:152998467-153208713	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1005012	chr2:153206764-153273886	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4664103	FMNL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153193800-153211000	Weak transcription	HSMMtube	muscle
2	chr2:153194200-153224400	Weak transcription	Aorta	Aorta
3	chr2:153194600-153210400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:153194600-153210400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr2:153194600-153214600	Weak transcription	Gastric	stomach
6	chr2:153196000-153224800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:153196600-153211800	Weak transcription	Small Intestine	intestine
8	chr2:153198200-153214000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:153198600-153214400	Weak transcription	Right Atrium	heart
10	chr2:153199400-153212200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:153199800-153211800	Weak transcription	Fetal Kidney	kidney
12	chr2:153200400-153211800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:153200400-153215200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:153200600-153210400	Weak transcription	Ovary	ovary
15	chr2:153200600-153225600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:153200800-153209200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:153200800-153210000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:153200800-153210400	Weak transcription	NHDF-Ad	bronchial
19	chr2:153200800-153210600	Weak transcription	Psoas Muscle	Psoas
20	chr2:153200800-153212600	Weak transcription	Fetal Intestine Large	intestine
21	chr2:153200800-153215800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:153200800-153222000	Weak transcription	Placenta	Placenta
23	chr2:153200800-153225800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:153201600-153216000	Weak transcription	Fetal Lung	lung
25	chr2:153202400-153211000	Weak transcription	NHEK	skin
26	chr2:153202400-153219800	Weak transcription	Hela-S3	cervix
27	chr2:153202400-153225600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:153203000-153223800	Weak transcription	Fetal Stomach	stomach
29	chr2:153203000-153233000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:153204400-153209200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:153205200-153209600	Weak transcription	A549	lung
32	chr2:153205200-153210600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:153205200-153210600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:153205200-153211400	Weak transcription	Adipose Nuclei	Adipose
35	chr2:153205200-153216000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:153205400-153210200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:153205400-153223800	Weak transcription	HMEC	breast
38	chr2:153206400-153210800	Weak transcription	Fetal Brain Female	brain
39	chr2:153206600-153214400	Weak transcription	Left Ventricle	heart
40	chr2:153206800-153210600	Weak transcription	Fetal Brain Male	brain
41	chr2:153206800-153215600	Weak transcription	Pancreas	Pancrea
42	chr2:153206800-153240800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:153207000-153209200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:153207000-153214400	Weak transcription	Lung	lung
45	chr2:153207000-153223200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:153207200-153209200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:153207200-153209800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:153207200-153210200	Enhancers	HepG2	liver
49	chr2:153207400-153210400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:153207600-153246400	Weak transcription	Fetal Intestine Small	intestine

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