Variant report

Variant	rs4886800
Chromosome Location	chr15:76678692-76678693
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr15:76678244-76679262	MCF-7	breast:	n/a	n/a
2	HDAC2	chr15:76678382-76678880	MCF-7	breast:	n/a	n/a
3	SIN3AK20	chr15:76678291-76679054	MCF-7	breast:	n/a	n/a
4	CEBPB	chr15:76678585-76678838	IMR90	lung:	n/a	n/a
5	FOSL2	chr15:76678404-76678899	MCF-7	breast:	n/a	n/a
6	ZNF217	chr15:76678516-76679081	MCF-7	breast:	n/a	n/a
7	GATA3	chr15:76678356-76679216	MCF-7	breast:	n/a	n/a
8	JUND	chr15:76678328-76678819	MCF-7	breast:	n/a	n/a
9	GATA3	chr15:76678446-76678866	MCF-7	breast:	n/a	n/a
10	JUND	chr15:76678335-76678840	MCF-7	breast:	n/a	n/a
11	JUND	chr15:76678202-76679019	T-47D	breast:	n/a	n/a
12	GABPA	chr15:76678385-76678886	MCF-7	breast:	n/a	n/a
13	EP300	chr15:76678394-76678819	T-47D	breast:	n/a	n/a
14	CEBPB	chr15:76678493-76678990	MCF-7	breast:	n/a	n/a
15	SIN3AK20	chr15:76678211-76679052	MCF-7	breast:	n/a	n/a
16	FOXA1	chr15:76678385-76678868	T-47D	breast:	n/a	n/a
17	NR2F2	chr15:76678265-76679068	MCF-7	breast:	n/a	n/a
18	NR2F2	chr15:76678269-76679042	MCF-7	breast:	n/a	n/a
19	EP300	chr15:76678319-76678909	T-47D	breast:	n/a	n/a
20	FOSL2	chr15:76678397-76679007	MCF-7	breast:	n/a	n/a
21	GATA3	chr15:76678301-76678919	T-47D	breast:	n/a	n/a
22	TCF7L2	chr15:76678386-76678867	MCF-7	breast:	n/a	n/a
23	FOS	chr15:76678557-76678865	MCF10A-Er-Src	breast:	n/a	n/a
24	HDAC2	chr15:76678322-76679021	MCF-7	breast:	n/a	n/a
25	FOXA1	chr15:76678412-76678799	T-47D	breast:	n/a	n/a
26	GATA3	chr15:76678221-76679035	MCF-7	breast:	n/a	n/a
27	GATA3	chr15:76678227-76678955	T-47D	breast:	n/a	n/a
28	FOS	chr15:76678596-76678865	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76677877..76679939-chr15:76693562..76695199,2	MCF-7	breast:
2	chr15:76626949..76629326-chr15:76677792..76680688,2	MCF-7	breast:

No data

Variant related genes	Relation type
SCAPER	TF binding region
ENSG00000159556	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11072591	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072597	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11072598	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11629888	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11632222	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11634019	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs11635463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11637490	0.81[ASN][1000 genomes]
rs11638767	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11856717	0.87[CHB][hapmap]
rs11857015	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11857327	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12437981	0.80[CEU][hapmap];0.87[CHB][hapmap]
rs12591100	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12900179	0.89[ASN][1000 genomes]
rs12903874	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12906143	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12909656	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs157783	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1607015	0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1607017	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2048856	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2280306	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2436994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2454450	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2454451	0.87[CHB][hapmap]
rs2454454	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2459361	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2461870	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2461871	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2461872	0.90[CHB][hapmap]
rs2468130	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2468131	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2469249	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs283789	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs283793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs283795	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs284891	0.80[ASN][1000 genomes]
rs284899	0.81[ASN][1000 genomes]
rs2944378	0.80[ASN][1000 genomes]
rs2957614	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3765115	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs437131	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4886488	0.83[JPT][hapmap]
rs4886493	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886495	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4886798	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886805	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4886816	0.80[CEU][hapmap];0.86[CHB][hapmap]
rs56246286	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62028380	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62028406	0.89[ASN][1000 genomes]
rs62028423	0.82[ASN][1000 genomes]
rs62028434	0.81[ASN][1000 genomes]
rs744336	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8029283	0.86[CHB][hapmap]
rs8037847	0.87[CHB][hapmap]
rs908817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs965818	0.87[CHB][hapmap]

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	nsv510667	chr15:76653359-76708310	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4886800	SCAPER	cis	Adipose Subcutaneous	GTEx
rs4886800	SCAPER	cis	Muscle Skeletal	GTEx
rs4886800	SCAPER	cis	Esophagus Mucosa	GTEx
rs4886800	SCAPER	cis	Nerve Tibial	GTEx
rs4886800	ZNF291	cis	lesional skin	skin_eQTL
rs4886800	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs4886800	SCAPER	cis	Artery Tibial	GTEx
rs4886800	SCAPER	cis	Esophagus Muscularis	GTEx
rs4886800	SCAPER	cis	Whole Blood	GTEx
rs4886800	SCAPER	cis	Thyroid	GTEx
rs4886800	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs4886800	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs4886800	SCAPER	cis	lung	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76639800-76682600	Weak transcription	Pancreas	Pancrea
2	chr15:76639800-76695400	Weak transcription	Spleen	Spleen
3	chr15:76639800-76727400	Weak transcription	Right Ventricle	heart
4	chr15:76640800-76694600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr15:76641400-76694600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:76642800-76693800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr15:76643800-76695000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:76645800-76686200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:76646600-76695400	Weak transcription	Ovary	ovary
10	chr15:76660800-76693600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:76661000-76685800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:76661000-76695200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:76661000-76695400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:76661000-76695400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:76661000-76708600	Weak transcription	Brain Anterior Caudate	brain
16	chr15:76661200-76698000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:76661200-76710800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:76661600-76698000	Weak transcription	Dnd41	blood
19	chr15:76662400-76679000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr15:76662400-76695400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr15:76662800-76679200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr15:76664800-76698000	Weak transcription	Brain Hippocampus Middle	brain
23	chr15:76666200-76679400	Weak transcription	Placenta	Placenta
24	chr15:76666200-76694600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:76666200-76696200	Weak transcription	Brain Angular Gyrus	brain
26	chr15:76666200-76706800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr15:76666400-76694600	Weak transcription	Adipose Nuclei	Adipose
28	chr15:76666400-76695200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr15:76666400-76695400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:76666400-76698200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr15:76666600-76695200	Weak transcription	Fetal Muscle Leg	muscle
32	chr15:76667200-76681600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr15:76668800-76679600	Weak transcription	Thymus	Thymus
34	chr15:76668800-76695000	Weak transcription	Fetal Brain Female	brain
35	chr15:76668800-76695400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr15:76669600-76695200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr15:76669800-76693600	Weak transcription	Fetal Intestine Large	intestine
38	chr15:76669800-76694200	Weak transcription	Psoas Muscle	Psoas
39	chr15:76670600-76683400	Weak transcription	HepG2	liver
40	chr15:76673200-76686000	Weak transcription	Fetal Stomach	stomach
41	chr15:76673200-76727400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr15:76673800-76694800	Weak transcription	Primary B cells from cord blood	blood
43	chr15:76674000-76682000	Weak transcription	Fetal Intestine Small	intestine
44	chr15:76674400-76695400	Weak transcription	Lung	lung
45	chr15:76674600-76680800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr15:76674600-76694800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr15:76674600-76718400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:76675200-76682800	Weak transcription	Aorta	Aorta
49	chr15:76675800-76696200	Weak transcription	Fetal Brain Male	brain
50	chr15:76677600-76680600	Strong transcription	Primary T cells from cord blood	blood

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