Variant report

Variant	rs16968730
Chromosome Location	chr15:77535785-77535786
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	chr15:77533789..77536624-chr15:77711955..77714562,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140382	Chromatin interaction
ENSG00000173517	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1015813	0.93[ASN][1000 genomes]
rs10519158	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs11853625	0.89[ASN][1000 genomes]
rs11854466	0.82[ASN][1000 genomes]
rs11856513	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs11856538	0.96[CEU][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs11857330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12148274	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324366	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12900110	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12902106	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12902434	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12902446	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12912963	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13380152	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1374201	0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs1446313	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17381652	0.96[CEU][hapmap];0.83[JPT][hapmap]
rs17381821	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs17383078	0.83[ASN][1000 genomes]
rs17385296	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs17466480	0.84[EUR][1000 genomes]
rs17468413	0.91[ASN][1000 genomes]
rs1867780	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs2044453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2137977	0.82[ASN][1000 genomes]
rs2292594	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs2864079	0.82[ASN][1000 genomes]
rs2864840	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs34572155	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4592615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4638539	0.82[ASN][1000 genomes]
rs4886514	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886852	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4886857	0.82[ASN][1000 genomes]
rs55881066	0.89[ASN][1000 genomes]
rs55994208	0.87[ASN][1000 genomes]
rs56070388	0.89[ASN][1000 genomes]
rs58792939	0.89[ASN][1000 genomes]
rs60079927	0.82[ASN][1000 genomes]
rs60761381	0.93[ASN][1000 genomes]
rs60863150	0.89[ASN][1000 genomes]
rs7163620	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7182221	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs74025104	0.89[ASN][1000 genomes]
rs74025105	0.82[ASN][1000 genomes]
rs74027548	0.89[ASN][1000 genomes]
rs74027549	0.91[ASN][1000 genomes]
rs7496431	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs9806326	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1832234	chr15:77451350-77694607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1041064	chr15:77497903-77631698	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1051744	chr15:77511489-77679160	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1044270	chr15:77534919-77611256	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv542445	chr15:77534919-77611256	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv1830237	chr15:77535785-77694607	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16968730	PSTPIP1	cis	multi-tissue	Pritchard
rs16968730	CYP1A2	cis	cerebellum	SCAN
rs16968730	HMG20A	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77492400-77544000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr15:77505800-77559400	Weak transcription	Psoas Muscle	Psoas
3	chr15:77508000-77543400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:77511200-77541800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:77517400-77559000	Weak transcription	Ovary	ovary
6	chr15:77517600-77543200	Weak transcription	HSMM	muscle
7	chr15:77517600-77545800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr15:77517800-77544200	Weak transcription	NHLF	lung
9	chr15:77519400-77551800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr15:77519600-77551800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:77519800-77557200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:77520000-77540000	Weak transcription	HUVEC	blood vessel
13	chr15:77520200-77578800	Weak transcription	Small Intestine	intestine
14	chr15:77523200-77544000	Weak transcription	Pancreas	Pancrea
15	chr15:77526400-77547600	Weak transcription	Liver	Liver
16	chr15:77526600-77538600	Weak transcription	Osteobl	bone
17	chr15:77527000-77559000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:77527000-77576200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr15:77528200-77544200	Weak transcription	NH-A	brain
20	chr15:77528400-77553000	Weak transcription	Aorta	Aorta
21	chr15:77528600-77544000	Weak transcription	Placenta	Placenta
22	chr15:77528800-77559200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:77528800-77571400	Weak transcription	Right Ventricle	heart
24	chr15:77528800-77574400	Weak transcription	HepG2	liver
25	chr15:77528800-77577200	Weak transcription	Spleen	Spleen
26	chr15:77528800-77579200	Weak transcription	Brain Angular Gyrus	brain
27	chr15:77529000-77540800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:77529000-77543800	Weak transcription	HSMMtube	muscle
29	chr15:77529000-77544200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr15:77529000-77544200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr15:77529000-77548600	Weak transcription	Gastric	stomach
32	chr15:77529200-77538600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr15:77529200-77540600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr15:77529200-77540800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:77529200-77541200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:77529200-77544000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr15:77529200-77544000	Weak transcription	Fetal Lung	lung
38	chr15:77529200-77545800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr15:77529200-77546400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr15:77529200-77546800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:77529200-77561400	Weak transcription	Primary T cells from cord blood	blood
42	chr15:77529400-77536000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:77529400-77538400	Weak transcription	Fetal Intestine Small	intestine
44	chr15:77529400-77538600	Weak transcription	Fetal Stomach	stomach
45	chr15:77529400-77539800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:77529400-77540400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:77529400-77540400	Weak transcription	Fetal Intestine Large	intestine
48	chr15:77529400-77540600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr15:77529400-77540600	Weak transcription	Left Ventricle	heart
50	chr15:77529400-77540800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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