Variant report

Variant	rs16864387
Chromosome Location	chr1:171283843-171283844
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	chr1:171283686..171286081-chr1:171289789..171292342,2	K562	blood:

Variant related genes	Relation type
ENSG00000076258	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10399602	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10399952	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10798297	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10912672	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10912673	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10912713	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10912714	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10912723	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912736	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1126692	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11484641	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11484642	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11487396	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12057955	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12058402	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059179	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12062692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12068552	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070766	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12072043	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077231	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077755	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12079141	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080449	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081291	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12091482	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12092985	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12094878	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141555	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12354390	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12726624	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12729885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730181	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742008	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745080	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12747080	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12755975	1.00[JPT][hapmap]
rs12757839	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];1.00[ASN][1000 genomes]
rs13376631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16864302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17581251	0.94[ASN][1000 genomes]
rs2006986	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2076322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2284130	1.00[JPT][hapmap]
rs2284131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28741369	1.00[ASN][1000 genomes]
rs34118031	1.00[ASN][1000 genomes]
rs34320519	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4607925	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55949630	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6424932	0.82[EUR][1000 genomes]
rs6670639	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6674596	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs742350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742351	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512853	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7519999	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7539057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7541377	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][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	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16864387	SELP	cis	cerebellum	SCAN
rs16864387	FMO4	cis	parietal	SCAN
rs16864387	FMO4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171266600-171288400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:171282400-171284200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:171282600-171284000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:171282600-171284200	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr1:171282800-171284000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:171282800-171284000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:171282800-171284000	Active TSS	Brain Hippocampus Middle	brain
8	chr1:171282800-171284000	Active TSS	Rectal Smooth Muscle	rectum
9	chr1:171282800-171284000	Active TSS	Right Atrium	heart
10	chr1:171282800-171284000	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr1:171282800-171284000	Active TSS	Stomach Smooth Muscle	stomach
12	chr1:171282800-171284200	Active TSS	Fetal Intestine Large	intestine
13	chr1:171282800-171284200	Enhancers	HepG2	liver
14	chr1:171282800-171284800	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr1:171283000-171284200	Active TSS	Duodenum Mucosa	Duodenum
16	chr1:171283200-171284000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:171283200-171284000	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr1:171283200-171284000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:171283200-171284000	Active TSS	Primary B cells from cord blood	blood
20	chr1:171283200-171284000	Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr1:171283200-171284000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:171283200-171284000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:171283200-171284000	Active TSS	Colonic Mucosa	Colon
24	chr1:171283200-171284000	Active TSS	Psoas Muscle	Psoas
25	chr1:171283200-171284000	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr1:171283200-171284000	Active TSS	Right Ventricle	heart
27	chr1:171283200-171284000	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr1:171283200-171284600	Active TSS	Liver	Liver
29	chr1:171283400-171284000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr1:171283400-171284000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr1:171283400-171284000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr1:171283400-171284000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:171283400-171284000	Active TSS	Ovary	ovary
34	chr1:171283400-171284200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:171283400-171284200	Active TSS	Aorta	Aorta
36	chr1:171283400-171284600	Active TSS	Fetal Intestine Small	intestine
37	chr1:171283400-171288000	Weak transcription	Small Intestine	intestine
38	chr1:171283600-171284000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:171283600-171284000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:171283600-171284000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr1:171283600-171284000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:171283600-171284000	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr1:171283600-171284000	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr1:171283600-171284000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr1:171283600-171284000	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr1:171283600-171284000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:171283600-171284000	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr1:171283600-171284000	Flanking Active TSS	Fetal Kidney	kidney
49	chr1:171283600-171284000	Flanking Active TSS	GM12878-XiMat	blood
50	chr1:171283600-171284000	Flanking Active TSS	HMEC	breast

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