Variant report

Variant	rs2404600
Chromosome Location	chr15:77173557-77173558
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: 40 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10851892	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072628	0.83[AFR][1000 genomes]
rs11072631	0.83[AFR][1000 genomes]
rs11072636	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072637	0.90[ASN][1000 genomes]
rs11635584	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11637296	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855296	0.83[AFR][1000 genomes]
rs12050866	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12903331	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12903586	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12909065	0.85[EUR][1000 genomes]
rs12913024	0.88[AFR][1000 genomes]
rs1567671	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2280194	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34450864	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34998733	0.83[AFR][1000 genomes]
rs35710279	0.83[AFR][1000 genomes]
rs35940181	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812908	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812909	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886506	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886840	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886842	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55817928	0.84[ASN][1000 genomes]
rs56275930	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495224	0.86[ASN][1000 genomes]
rs907593	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs907594	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9707794	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2404600	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs2404600	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs2404600	SCAPER	cis	Thyroid	GTEx
rs2404600	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs2404600	SCAPER	cis	Artery Tibial	GTEx
rs2404600	SCAPER	cis	Nerve Tibial	GTEx
rs2404600	SCAPER	cis	Adipose Subcutaneous	GTEx
rs2404600	SCAPER	cis	Whole Blood	GTEx
rs2404600	SCAPER	cis	lung	GTEx
rs2404600	SCAPER	cis	Muscle Skeletal	GTEx
rs2404600	SCAPER	cis	Esophagus Muscularis	GTEx
rs2404600	SCAPER	cis	Esophagus Mucosa	GTEx

Chromatin state (count:87 , 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	chr15:77164800-77173800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr15:77166200-77175400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr15:77166800-77177800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr15:77167600-77177200	Weak transcription	Hela-S3	cervix
36	chr15:77168000-77174800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr15:77168000-77179600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:77168000-77179600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:77168200-77177400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr15:77168400-77179400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:77168400-77195000	Weak transcription	Adipose Nuclei	Adipose
42	chr15:77168600-77173600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr15:77168600-77173600	Weak transcription	Placenta	Placenta
44	chr15:77168600-77174000	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr15:77168600-77174400	Weak transcription	Fetal Intestine Large	intestine
46	chr15:77168600-77175800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:77168600-77177200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr15:77168600-77178000	Weak transcription	Gastric	stomach
49	chr15:77168600-77179600	Weak transcription	Lung	lung
50	chr15:77168600-77180000	Weak transcription	Esophagus	oesophagus

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