Variant report

Variant	rs16958019
Chromosome Location	chr15:73860318-73860319
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:73858288..73861135-chr15:73861211..73863696,2	MCF-7	breast:
2	chr15:73860177..73862340-chr15:73865133..73867086,2	MCF-7	breast:
3	chr15:73859098..73862210-chr15:73922797..73926936,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C15orf59-5	chr15:73859279-73861884	NONHSAT047148

Variant related genes	Relation type
ENSG00000156642	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10152645	0.88[JPT][hapmap]
rs10162605	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10163172	0.86[EUR][1000 genomes]
rs1044581	0.88[JPT][hapmap]
rs11072433	0.88[JPT][hapmap]
rs11574484	0.88[JPT][hapmap]
rs11574485	0.88[JPT][hapmap]
rs11638472	0.82[EUR][1000 genomes]
rs11854138	0.82[CEU][hapmap]
rs11854774	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11856313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324832	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12908815	0.86[EUR][1000 genomes]
rs13380155	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13380245	0.86[ASW][hapmap];0.82[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1481087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16957919	0.80[EUR][1000 genomes]
rs16957997	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16958025	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16958041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16958050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291012	0.88[JPT][hapmap]
rs2291014	0.88[JPT][hapmap]
rs2306462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2415153	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28834466	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3889590	0.82[EUR][1000 genomes]
rs55636021	0.86[EUR][1000 genomes]
rs55695286	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56190024	0.86[EUR][1000 genomes]
rs56227598	0.82[EUR][1000 genomes]
rs57995256	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60419012	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6495066	0.82[EUR][1000 genomes]
rs7163212	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7163693	0.85[CEU][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7164953	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7165447	0.82[CEU][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7166673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169976	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes]
rs7172448	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7173068	0.82[EUR][1000 genomes]
rs7176174	0.88[JPT][hapmap]
rs7176452	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7176484	0.88[JPT][hapmap]
rs7176701	0.88[JPT][hapmap]
rs7177731	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap]
rs7177814	0.88[JPT][hapmap]
rs7178133	0.88[JPT][hapmap]
rs7178806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7182876	0.88[JPT][hapmap]
rs729155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8027255	0.82[EUR][1000 genomes]
rs8028749	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8032265	0.82[CEU][hapmap]
rs8033242	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs8036438	0.85[CEU][hapmap]
rs8039862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8040552	0.81[ASN][1000 genomes]
rs899271	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037540	chr15:73712637-73982420	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv904344	chr15:73800519-73864831	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73844200-73863800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:73844800-73865200	Weak transcription	Stomach Mucosa	stomach
3	chr15:73846200-73863800	Strong transcription	Duodenum Mucosa	Duodenum
4	chr15:73846400-73863200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr15:73847400-73862000	Strong transcription	Fetal Intestine Large	intestine
6	chr15:73847400-73866000	Strong transcription	Adipose Nuclei	Adipose
7	chr15:73847400-73893200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:73847600-73865000	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr15:73847600-73865400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:73847600-73865800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:73847600-73866200	Strong transcription	Liver	Liver
12	chr15:73847600-73882400	Strong transcription	Placenta	Placenta
13	chr15:73848000-73860600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr15:73848600-73860600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:73848600-73868600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr15:73848600-73868600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:73848800-73861000	Weak transcription	Small Intestine	intestine
18	chr15:73848800-73884800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr15:73848800-73885000	Strong transcription	Primary B cells from cord blood	blood
20	chr15:73849400-73860400	Weak transcription	Pancreas	Pancrea
21	chr15:73850000-73868600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr15:73850200-73861600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr15:73850200-73884400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:73850400-73866200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:73850400-73870800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr15:73851200-73861000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr15:73852200-73861200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:73852200-73861600	Weak transcription	Fetal Brain Male	brain
29	chr15:73852200-73874600	Weak transcription	Fetal Heart	heart
30	chr15:73853400-73864200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr15:73853400-73869000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:73853800-73860800	Weak transcription	Fetal Kidney	kidney
33	chr15:73853800-73868600	Strong transcription	Primary T cells from cord blood	blood
34	chr15:73855200-73867000	Strong transcription	GM12878-XiMat	blood
35	chr15:73855400-73869200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:73855800-73865000	Strong transcription	Spleen	Spleen
37	chr15:73855800-73868200	Weak transcription	Psoas Muscle	Psoas
38	chr15:73855800-73872400	Strong transcription	Fetal Stomach	stomach
39	chr15:73856200-73861600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:73856200-73863000	Strong transcription	Fetal Intestine Small	intestine
41	chr15:73856400-73878000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr15:73856600-73860600	Weak transcription	Brain Germinal Matrix	brain
43	chr15:73856800-73861800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr15:73857000-73865600	Strong transcription	Rectal Smooth Muscle	rectum
45	chr15:73857200-73860400	Weak transcription	NH-A	brain
46	chr15:73857200-73860600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr15:73857200-73860800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr15:73857200-73861000	Weak transcription	Brain Substantia Nigra	brain
49	chr15:73857200-73865800	Strong transcription	HMEC	breast
50	chr15:73857200-73868600	Strong transcription	A549	lung

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