Variant report

Variant	rs7169663
Chromosome Location	chr15:77192843-77192844
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77192531..77194476-chr15:77194873..77197873,3	K562	blood:
2	chr15:77190700..77193071-chr15:77213963..77216212,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140386	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1116535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12148386	0.85[ASN][1000 genomes]
rs12438362	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12441484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs12441855	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904198	0.80[AMR][1000 genomes]
rs12909665	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12910734	0.80[AMR][1000 genomes]
rs12911174	0.80[AMR][1000 genomes]
rs12912465	0.85[YRI][hapmap]
rs12913810	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916324	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1471780	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17380507	0.88[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17464903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2137307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs2304920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2404602	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2469204	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs34338978	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34748201	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35076986	1.00[ASN][1000 genomes]
rs35157989	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35170561	0.80[AMR][1000 genomes]
rs35999717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3829489	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4360890	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]
rs4383105	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4442773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4641709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4886503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs4886507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886829	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4886839	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55864032	0.80[AMR][1000 genomes]
rs56234001	0.92[ASN][1000 genomes]
rs58889902	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66508953	0.86[ASN][1000 genomes]
rs66866130	0.80[AMR][1000 genomes]
rs71398948	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166156	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs8024737	0.86[ASN][1000 genomes]
rs8028294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs8040539	0.86[JPT][hapmap]
rs9788684	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
rs7169663	SCAPER	cis	Artery Tibial	GTEx
rs7169663	SCAPER	cis	Thyroid	GTEx
rs7169663	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs7169663	SCAPER	cis	lung	GTEx
rs7169663	SCAPER	cis	Nerve Tibial	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77112200-77196000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr15:77133200-77196800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr15:77140800-77195800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:77142000-77195800	Weak transcription	Right Ventricle	heart
5	chr15:77146400-77196400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:77148600-77195600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr15:77148800-77195600	Weak transcription	Dnd41	blood
8	chr15:77158800-77195600	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:77158800-77195600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr15:77168400-77195000	Weak transcription	Adipose Nuclei	Adipose
11	chr15:77168600-77195000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:77168600-77195600	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:77168600-77196800	Weak transcription	Pancreas	Pancrea
14	chr15:77168600-77196800	Weak transcription	Spleen	Spleen
15	chr15:77172800-77195600	Weak transcription	HSMM	muscle
16	chr15:77175600-77196800	Weak transcription	Aorta	Aorta
17	chr15:77175600-77196800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr15:77175800-77195600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:77176000-77195800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr15:77176000-77196800	Weak transcription	Ovary	ovary
21	chr15:77176200-77195400	Weak transcription	Primary B cells from cord blood	blood
22	chr15:77176200-77195800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr15:77176400-77195600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr15:77179400-77196000	Weak transcription	Thymus	Thymus
25	chr15:77179800-77195600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr15:77180000-77196800	Weak transcription	Lung	lung
27	chr15:77184400-77195800	Weak transcription	Primary T cells from cord blood	blood
28	chr15:77186800-77195400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr15:77186800-77195400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:77186800-77195800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:77187800-77195400	Weak transcription	GM12878-XiMat	blood
32	chr15:77189000-77195600	Weak transcription	Brain Substantia Nigra	brain
33	chr15:77189200-77194400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr15:77189200-77195400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:77189200-77196800	Weak transcription	Gastric	stomach
36	chr15:77190200-77196800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:77190200-77196800	Weak transcription	Esophagus	oesophagus
38	chr15:77190600-77194800	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr15:77191000-77196800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr15:77191200-77195200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr15:77191200-77195200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:77191200-77195600	Weak transcription	NHEK	skin
43	chr15:77191200-77195800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr15:77191200-77195800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:77191600-77196600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:77191800-77194800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:77191800-77195600	Weak transcription	Placenta	Placenta
48	chr15:77191800-77195800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:77191800-77196000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr15:77192000-77196600	Weak transcription	Fetal Stomach	stomach

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