Variant report

Variant	rs1981916
Chromosome Location	chr15:62171479-62171480
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	chr15:62170697..62173317-chr15:62182241..62184749,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1000598	0.89[CEU][hapmap];0.83[JPT][hapmap]
rs11071642	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs11631970	0.85[CEU][hapmap];0.83[JPT][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs11635569	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12437684	0.86[EUR][1000 genomes]
rs12439934	0.81[CEU][hapmap]
rs12708470	0.85[CEU][hapmap];0.83[JPT][hapmap];0.92[LWK][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12901481	0.85[CEU][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12906423	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12908081	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12908182	0.84[EUR][1000 genomes]
rs12908472	0.89[EUR][1000 genomes]
rs12911564	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12912208	0.85[CEU][hapmap]
rs12915295	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12915825	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12916268	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13379492	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13379947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1346035	0.81[EUR][1000 genomes]
rs1346037	0.81[EUR][1000 genomes]
rs1425270	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1436966	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs17205225	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17271144	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17271151	0.85[CEU][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap]
rs17271158	0.81[EUR][1000 genomes]
rs17271193	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17271340	0.85[CEU][hapmap]
rs1981917	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2414753	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs2414755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28373613	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28411984	0.90[EUR][1000 genomes]
rs34965045	0.89[EUR][1000 genomes]
rs3743297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3784634	0.81[CEU][hapmap]
rs3809517	0.84[CEU][hapmap]
rs4283171	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4587915	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4774422	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4774427	0.89[CEU][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs4775453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7166891	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7170293	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7172145	0.85[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.97[LWK][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7172967	0.88[CEU][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs7179506	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs748669	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8029942	0.85[CEU][hapmap]
rs8032681	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8033816	0.83[TSI][hapmap]
rs8034185	0.85[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes]
rs8034216	0.85[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs8034335	0.85[CEU][hapmap];0.83[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs8039105	0.85[CEU][hapmap]
rs963024	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904284	chr15:62123600-62243197	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv521334	chr15:62129809-62340126	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv527451	chr15:62129809-62340126	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv904285	chr15:62146598-62246864	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv904286	chr15:62146598-62313373	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv904287	chr15:62146598-62338797	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv904288	chr15:62146598-62356386	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv569641	chr15:62155282-62287456	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv904289	chr15:62156690-62287456	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1981916	VPS13C	cis	cerebellum	SCAN
rs1981916	CA12	cis	cerebellum	SCAN
rs1981916	FAM81A	cis	cerebellum	SCAN
rs1981916	TPM1	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62138800-62184200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:62139200-62182200	Weak transcription	Brain Substantia Nigra	brain
3	chr15:62139800-62185200	Weak transcription	NHLF	lung
4	chr15:62140000-62184800	Weak transcription	Right Ventricle	heart
5	chr15:62140200-62180000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:62142000-62209400	Weak transcription	Colonic Mucosa	Colon
7	chr15:62142400-62253000	Weak transcription	Spleen	Spleen
8	chr15:62142600-62209200	Weak transcription	K562	blood
9	chr15:62143800-62182200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:62143800-62235600	Weak transcription	Fetal Brain Male	brain
11	chr15:62144000-62194600	Weak transcription	Fetal Lung	lung
12	chr15:62144800-62184000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:62145200-62182000	Weak transcription	NHEK	skin
14	chr15:62145400-62171600	Weak transcription	Stomach Mucosa	stomach
15	chr15:62145800-62182000	Weak transcription	Small Intestine	intestine
16	chr15:62146800-62230000	Weak transcription	Pancreas	Pancrea
17	chr15:62147000-62181800	Weak transcription	Brain Anterior Caudate	brain
18	chr15:62147000-62184000	Weak transcription	Lung	lung
19	chr15:62147800-62184000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:62149000-62198000	Weak transcription	Fetal Kidney	kidney
21	chr15:62150000-62276200	Weak transcription	Psoas Muscle	Psoas
22	chr15:62150200-62184200	Weak transcription	Aorta	Aorta
23	chr15:62150200-62185400	Weak transcription	Fetal Heart	heart
24	chr15:62150800-62182000	Weak transcription	HSMMtube	muscle
25	chr15:62150800-62183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr15:62153200-62185400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr15:62153800-62185000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:62154200-62198200	Weak transcription	NH-A	brain
29	chr15:62154400-62184200	Weak transcription	Fetal Intestine Small	intestine
30	chr15:62154600-62183800	Weak transcription	Brain Angular Gyrus	brain
31	chr15:62154800-62184200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:62155000-62184600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:62158200-62175200	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr15:62158600-62176400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr15:62159200-62174600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr15:62159200-62175200	Strong transcription	Primary B cells from cord blood	blood
37	chr15:62159400-62175000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:62160400-62172200	Weak transcription	Brain Germinal Matrix	brain
39	chr15:62161800-62184200	Weak transcription	Fetal Brain Female	brain
40	chr15:62162200-62175200	Strong transcription	Dnd41	blood
41	chr15:62162600-62195200	Weak transcription	Fetal Stomach	stomach
42	chr15:62163000-62181800	Weak transcription	A549	lung
43	chr15:62163000-62182400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:62163000-62184800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr15:62163000-62198400	Weak transcription	Osteobl	bone
46	chr15:62163200-62180200	Weak transcription	NHDF-Ad	bronchial
47	chr15:62163400-62184000	Weak transcription	Fetal Muscle Leg	muscle
48	chr15:62163600-62184800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:62163800-62181600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:62163800-62181800	Weak transcription	Brain Cingulate Gyrus	brain

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