Variant report

Variant	rs4360890
Chromosome Location	chr15:77173295-77173296
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77164850..77168974-chr15:77171197..77173807,3	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1116535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12148386	0.82[ASN][1000 genomes]
rs12437733	0.80[EUR][1000 genomes]
rs12438362	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12441484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs12441855	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594556	0.81[EUR][1000 genomes]
rs12595586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904198	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12909665	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12910734	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12911174	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12912465	0.85[YRI][hapmap]
rs12913810	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916324	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471780	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs17367297	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17380507	0.89[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17464903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2137307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2304920	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs2404602	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2469204	0.88[CHB][hapmap]
rs3110382	0.81[EUR][1000 genomes]
rs34338978	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34748201	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35076986	0.97[ASN][1000 genomes]
rs35157989	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35170561	0.80[AMR][1000 genomes]
rs35999717	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3816266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs3829489	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4383105	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs4442773	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4641709	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs4886503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs4886507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886829	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4886839	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55864032	0.80[AMR][1000 genomes]
rs56234001	0.89[ASN][1000 genomes]
rs58889902	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66508953	0.83[ASN][1000 genomes]
rs66866130	0.80[AMR][1000 genomes]
rs71398948	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7166156	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7169663	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7174673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs7342603	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs7350777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs8024476	1.00[CEU][hapmap]
rs8024737	0.83[ASN][1000 genomes]
rs8028294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs8040539	0.86[JPT][hapmap]
rs8043474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs9788684	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	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
3	esv2830013	chr15:76863023-77176158	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1046137	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv542442	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1803942	chr15:77151005-77210457	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	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
9	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4360890	SCAPER	cis	Nerve Tibial	GTEx
rs4360890	SCAPER	cis	Thyroid	GTEx
rs4360890	SCAPER	cis	lung	GTEx
rs4360890	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs4360890	SCAPER	cis	Artery Tibial	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77111600-77174200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr15:77112200-77196000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr15:77125800-77175400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:77133200-77196800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:77140800-77195800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:77142000-77175800	Weak transcription	Fetal Brain Male	brain
7	chr15:77142000-77195800	Weak transcription	Right Ventricle	heart
8	chr15:77144800-77179000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:77146200-77175400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr15:77146400-77196400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:77147800-77173800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr15:77147800-77177200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:77148200-77175200	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:77148400-77174800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:77148600-77195600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:77148800-77181000	Weak transcription	Fetal Kidney	kidney
17	chr15:77148800-77195600	Weak transcription	Dnd41	blood
18	chr15:77154400-77179600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr15:77156400-77176400	Weak transcription	Psoas Muscle	Psoas
20	chr15:77158200-77174000	Weak transcription	Brain Anterior Caudate	brain
21	chr15:77158600-77175400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:77158600-77179800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:77158600-77180600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr15:77158600-77190800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:77158800-77175400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr15:77158800-77177800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr15:77158800-77195600	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:77158800-77195600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr15:77159400-77176800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr15:77161400-77188800	Weak transcription	Fetal Heart	heart
31	chr15:77161800-77174400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:77163600-77173400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr15:77164400-77173400	Weak transcription	Fetal Thymus	thymus
34	chr15:77164800-77173800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr15:77166200-77175400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr15:77166800-77177800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr15:77167600-77177200	Weak transcription	Hela-S3	cervix
38	chr15:77168000-77174800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr15:77168000-77179600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:77168000-77179600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:77168200-77177400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr15:77168400-77179400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:77168400-77195000	Weak transcription	Adipose Nuclei	Adipose
44	chr15:77168600-77173400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:77168600-77173400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr15:77168600-77173400	Weak transcription	Left Ventricle	heart
47	chr15:77168600-77173400	Weak transcription	Thymus	Thymus
48	chr15:77168600-77173600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr15:77168600-77173600	Weak transcription	Placenta	Placenta
50	chr15:77168600-77174000	Weak transcription	Monocytes-CD14+_RO01746	blood

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