Variant report

Variant	rs2280306
Chromosome Location	chr15:76652258-76652259
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:76651115..76653988-chr15:76656127..76658474,2	MCF-7	breast:
2	chr15:76651211..76653723-chr15:76658057..76660329,2	K562	blood:
3	chr15:76651584..76653764-chr15:76658090..76659845,2	MCF-7	breast:
4	chr15:76627109..76630617-chr15:76650461..76653550,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159556	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs11072591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11072598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11629888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11632222	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11634019	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11634060	0.82[CEU][hapmap]
rs11635463	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11637490	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11638767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855999	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11856717	0.87[CHB][hapmap]
rs11857015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12437981	0.95[CEU][hapmap];0.87[CHB][hapmap]
rs12591100	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12900179	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12903874	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12906143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12909656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs157783	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1607015	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1607017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2003344	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2048856	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2436994	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2436996	0.81[EUR][1000 genomes]
rs2454450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs2454454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2459361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2461870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2461871	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2461872	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs2468130	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2468131	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2469249	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs283789	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs283793	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs283795	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs284899	0.83[EUR][1000 genomes]
rs2957614	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3765115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs437131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4886488	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs4886493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886791	0.82[CEU][hapmap]
rs4886795	0.84[AMR][1000 genomes]
rs4886798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886800	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56246286	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62028380	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62028406	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62028423	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62028434	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71405204	0.89[AMR][1000 genomes]
rs744336	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8029283	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs908817	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525769	chr15:76632487-76661925	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2280306	ZNF291	cis	lesional skin	skin_eQTL
rs2280306	ZNF291	cis	uninvolved skin	skin_eQTL
rs2280306	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs2280306	SCAPER	cis	Thyroid	GTEx
rs2280306	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs2280306	SCAPER	cis	Esophagus Mucosa	GTEx
rs2280306	SCAPER	cis	Nerve Tibial	GTEx
rs2280306	ISL2	cis	Whole Blood	GTEx
rs2280306	SCAPER	cis	Adipose Subcutaneous	GTEx
rs2280306	SCAPER	cis	Whole Blood	GTEx
rs2280306	SCAPER	cis	Esophagus Muscularis	GTEx
rs2280306	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs2280306	SCAPER	cis	Artery Tibial	GTEx
rs2280306	SCAPER	cis	lung	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76639800-76659800	Weak transcription	Gastric	stomach
2	chr15:76639800-76682600	Weak transcription	Pancreas	Pancrea
3	chr15:76639800-76695400	Weak transcription	Spleen	Spleen
4	chr15:76639800-76727400	Weak transcription	Right Ventricle	heart
5	chr15:76640200-76658800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr15:76640800-76664400	Weak transcription	Brain Angular Gyrus	brain
7	chr15:76640800-76694600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr15:76641200-76659000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:76641400-76694600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:76641600-76665400	Weak transcription	Placenta	Placenta
11	chr15:76641800-76660400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr15:76641800-76673400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:76642000-76660400	Weak transcription	Esophagus	oesophagus
14	chr15:76642200-76652800	Weak transcription	Left Ventricle	heart
15	chr15:76642200-76664400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr15:76642400-76660400	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:76642800-76664600	Weak transcription	Thymus	Thymus
18	chr15:76642800-76693800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:76643800-76672400	Weak transcription	Primary B cells from cord blood	blood
20	chr15:76643800-76695000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr15:76644600-76664400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:76644600-76664600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:76644800-76664600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr15:76645800-76686200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:76646600-76664400	Weak transcription	Fetal Intestine Large	intestine
26	chr15:76646600-76695400	Weak transcription	Ovary	ovary
27	chr15:76646800-76659200	Weak transcription	Liver	Liver
28	chr15:76646800-76659400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:76646800-76666000	Weak transcription	Fetal Brain Female	brain
30	chr15:76647000-76656000	Weak transcription	Fetal Stomach	stomach
31	chr15:76647000-76660200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr15:76647000-76664600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr15:76648400-76652800	Strong transcription	Primary T cells from cord blood	blood
34	chr15:76648400-76668400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr15:76648400-76674400	Weak transcription	Brain Substantia Nigra	brain
36	chr15:76648800-76659200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr15:76649400-76659800	Weak transcription	Fetal Heart	heart
38	chr15:76650000-76660400	Weak transcription	Fetal Muscle Leg	muscle
39	chr15:76650400-76664400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr15:76650800-76674000	Weak transcription	Small Intestine	intestine
41	chr15:76651200-76652600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr15:76651400-76652400	Strong transcription	Brain Germinal Matrix	brain
43	chr15:76651800-76659200	Weak transcription	Lung	lung
44	chr15:76652000-76658000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr15:76652000-76660400	Weak transcription	Adipose Nuclei	Adipose
46	chr15:76652200-76655600	Weak transcription	Fetal Intestine Small	intestine
47	chr15:76652200-76656600	Weak transcription	Aorta	Aorta

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