Variant report

Variant	rs2280194
Chromosome Location	chr15:77239651-77239652
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:77232270..77234258-chr15:77239460..77241274,2	K562	blood:
2	chr15:77234332..77235848-chr15:77239349..77241797,2	K562	blood:
3	chr15:77238595..77241384-chr15:77923976..77926830,2	MCF-7	breast:
4	chr15:77230977..77234854-chr15:77238676..77241282,3	MCF-7	breast:
5	chr15:77237726..77241253-chr15:77241760..77244409,3	K562	blood:
6	chr15:77237875..77240141-chr15:77253920..77256491,2	MCF-7	breast:
7	chr15:77224081..77226260-chr15:77238341..77240662,2	MCF-7	breast:
8	chr15:77237726..77240574-chr15:77240909..77244202,4	K562	blood:
9	chr15:77235186..77238414-chr15:77239445..77241640,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169783	Chromatin interaction
ENSG00000117906	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10851892	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11072619	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs11072625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs11072626	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11072631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11072632	0.82[CHB][hapmap]
rs11072636	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11072637	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11633869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs11634266	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11634428	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs11635584	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11637296	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11852395	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs11855296	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs11855534	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs12050866	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12439141	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12898416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12903331	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12903586	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12904149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12909065	0.85[EUR][1000 genomes]
rs1443115	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1484990	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1567671	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404600	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34450864	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35940181	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3764245	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3812908	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3812909	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4312276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4886506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap]
rs4886840	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886842	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55817928	0.89[ASN][1000 genomes]
rs56275930	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495224	0.84[ASN][1000 genomes]
rs7178250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8025991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs907593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs907594	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9635380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs9707794	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs2280194	SCAPER	cis	Esophagus Mucosa	GTEx
rs2280194	ZNF291	cis	uninvolved skin	skin_eQTL
rs2280194	SCAPER	cis	cerebellum	SCAN
rs2280194	SCAPER	cis	Stomach	GTEx
rs2280194	SCAPER	cis	Artery Tibial	GTEx
rs2280194	SCAPER	cis	lymphoblastoid	seeQTL
rs2280194	ISL2	cis	lymphoblastoid	seeQTL
rs2280194	SCAPER	cis	Nerve Tibial	GTEx
rs2280194	SCAPER	cis	Adipose Subcutaneous	GTEx
rs2280194	NRG4	cis	parietal	SCAN
rs2280194	SCAPER	cis	lung	GTEx
rs2280194	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs2280194	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs2280194	ZNF291	cis	lesional skin	skin_eQTL
rs2280194	ISL2	cis	Whole Blood	GTEx
rs2280194	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs2280194	SCAPER	cis	Esophagus Muscularis	GTEx
rs2280194	SCAPER	cis	Whole Blood	GTEx
rs2280194	SCAPER	cis	parietal	SCAN
rs2280194	SCAPER	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77224800-77243000	Weak transcription	Lung	lung
2	chr15:77224800-77256000	Weak transcription	Pancreas	Pancrea
3	chr15:77225000-77240400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr15:77225000-77240400	Weak transcription	Spleen	Spleen
5	chr15:77225000-77241000	Weak transcription	Colonic Mucosa	Colon
6	chr15:77225000-77242800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:77225000-77243000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr15:77225000-77245200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:77225000-77245200	Weak transcription	Esophagus	oesophagus
10	chr15:77225000-77247000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:77225000-77254600	Weak transcription	Aorta	Aorta
12	chr15:77225000-77260200	Weak transcription	Right Ventricle	heart
13	chr15:77225200-77245200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:77225200-77246400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr15:77225400-77255400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr15:77225600-77243600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr15:77225800-77243800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:77225800-77244600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:77225800-77245000	Weak transcription	Fetal Heart	heart
20	chr15:77226200-77247200	Weak transcription	Fetal Brain Male	brain
21	chr15:77228200-77243000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:77228200-77245600	Weak transcription	HMEC	breast
23	chr15:77229200-77240800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr15:77229200-77243400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr15:77229200-77245200	Weak transcription	Small Intestine	intestine
26	chr15:77229200-77251600	Weak transcription	NHLF	lung
27	chr15:77229400-77239800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:77229400-77240200	Weak transcription	Hela-S3	cervix
29	chr15:77229400-77240600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr15:77229400-77240800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr15:77229400-77243000	Weak transcription	Left Ventricle	heart
32	chr15:77229400-77243200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr15:77229400-77249000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr15:77229400-77254400	Weak transcription	Psoas Muscle	Psoas
35	chr15:77229400-77255000	Weak transcription	Gastric	stomach
36	chr15:77229600-77243600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:77230200-77245400	Weak transcription	K562	blood
38	chr15:77231000-77240200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:77231400-77240600	Weak transcription	HSMMtube	muscle
40	chr15:77231400-77240800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr15:77231400-77242800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:77231400-77246400	Weak transcription	GM12878-XiMat	blood
43	chr15:77231400-77251800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:77231600-77242800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:77231600-77247200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:77233400-77243600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:77233800-77253400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:77234200-77243800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:77234400-77243400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:77234600-77241800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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