Variant report

Variant	rs16832913
Chromosome Location	chr1:161354980-161354981
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161350529..161353664-chr1:161354181..161356756,3	K562	blood:
2	chr1:161354244..161356268-chr1:161357860..161359450,2	K562	blood:
3	chr1:161140294..161141982-chr1:161353302..161356192,2	K562	blood:
4	chr1:161339110..161342306-chr1:161354763..161357671,3	K562	blood:
5	chr1:161333138..161335243-chr1:161353873..161355645,2	K562	blood:
6	chr1:161354632..161358747-chr1:161408665..161411829,3	K562	blood:
7	chr1:161351090..161356215-chr1:161358922..161361757,5	MCF-7	breast:

No data

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11577663	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578160	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579939	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580931	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583870	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584714	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585941	1.00[ASW][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16832786	1.00[MEX][hapmap];0.89[TSI][hapmap]
rs16832847	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16832849	0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16832911	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16832945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4272646	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656296	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55857747	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6427589	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678315	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs72714971	0.86[AMR][1000 genomes]
rs72714973	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714981	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714982	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714983	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72714985	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715002	0.83[AMR][1000 genomes]
rs7519821	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538701	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9793329	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432986	chr1:161221133-161673682	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1010776	chr1:161282384-161409218	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv432998	chr1:161335902-161673682	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv872493	chr1:161339060-161413794	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv433009	chr1:161343927-161639328	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
6	nsv1005812	chr1:161343951-161548101	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv535182	chr1:161343951-161548101	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
8	esv2756866	chr1:161344255-161681552	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
9	esv2758972	chr1:161344255-161681552	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
10	nsv998957	chr1:161353351-161398414	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16832913	PMF1	cis	cerebellum	SCAN
rs16832913	TTC24	cis	parietal	SCAN
rs16832913	SEMA4A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161328400-161359000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:161328600-161359000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:161335000-161356000	Weak transcription	K562	blood
4	chr1:161337800-161356200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:161338000-161356000	Weak transcription	GM12878-XiMat	blood
6	chr1:161349200-161358600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:161351800-161358800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:161352400-161355600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:161352400-161358600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:161352400-161358800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:161352600-161359200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:161352600-161359200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:161352800-161356000	Weak transcription	HepG2	liver
14	chr1:161352800-161359200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:161353000-161359200	Weak transcription	HUVEC	blood vessel
16	chr1:161353000-161359200	Weak transcription	NHLF	lung
17	chr1:161353400-161356200	Weak transcription	A549	lung
18	chr1:161353400-161359000	Weak transcription	Adipose Nuclei	Adipose
19	chr1:161353400-161359200	Weak transcription	Osteobl	bone
20	chr1:161353800-161356200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:161353800-161358600	Weak transcription	Hela-S3	cervix
22	chr1:161353800-161358800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:161353800-161358800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:161353800-161358800	Weak transcription	HMEC	breast
25	chr1:161353800-161359200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:161354000-161358600	Weak transcription	NHEK	skin
27	chr1:161354000-161359200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:161354600-161359200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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