Variant report

Variant	rs2235193
Chromosome Location	chr1:171108836-171108837
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10911839	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10911841	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10912425	0.89[ASN][1000 genomes]
rs11811455	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16864096	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1920144	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920151	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1920152	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1920153	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1920154	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2064079	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2064080	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236872	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2236873	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2281003	0.81[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4916390	0.88[ASN][1000 genomes]
rs58365744	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67522662	0.89[ASN][1000 genomes]
rs7881379	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7885012	0.89[ASN][1000 genomes]
rs909530	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2235193	FMO2	cis	Adipose Subcutaneous	GTEx
rs2235193	RP1-127D3.4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171091600-171109000	Weak transcription	Right Ventricle	heart
2	chr1:171105400-171111200	Weak transcription	Aorta	Aorta
3	chr1:171105800-171110400	Enhancers	Fetal Lung	lung
4	chr1:171106400-171110400	Enhancers	Adipose Nuclei	Adipose
5	chr1:171106800-171109000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:171107000-171110200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:171107200-171110200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:171107200-171110800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:171107200-171111200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:171107200-171111200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:171107200-171111400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:171107200-171111400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:171107400-171109200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:171107600-171109000	Weak transcription	Left Ventricle	heart
15	chr1:171107600-171109000	Weak transcription	Right Atrium	heart
16	chr1:171107600-171109000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:171107800-171109000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:171107800-171109000	Weak transcription	Stomach Mucosa	stomach
19	chr1:171107800-171110400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:171107800-171112400	Enhancers	Fetal Muscle Leg	muscle
21	chr1:171108000-171112600	Weak transcription	Small Intestine	intestine
22	chr1:171108400-171112800	Enhancers	NHLF	lung
23	chr1:171108600-171109200	Weak transcription	Brain Substantia Nigra	brain
24	chr1:171108800-171109200	Enhancers	Psoas Muscle	Psoas
25	chr1:171108800-171110200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:171108800-171111000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr1:171108800-171112400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:171108800-171112800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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