Variant report

Variant	rs1655556
Chromosome Location	chr15:41777935-41777936
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41773035..41782898-chr15:41783132..41789747,15	K562	blood:
2	chr15:41777763..41779575-chr15:41786284..41787961,2	MCF-7	breast:
3	chr15:41777253..41780203-chr15:41850412..41852434,2	K562	blood:
4	chr15:41768860..41771518-chr15:41776158..41779055,4	K562	blood:

Variant related genes	Relation type
ENSG00000137825	Chromatin interaction
ENSG00000092445	Chromatin interaction
ENSG00000137815	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11630191	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11631770	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1622914	0.82[EUR][1000 genomes]
rs1655557	0.85[EUR][1000 genomes]
rs16971798	0.81[EUR][1000 genomes]
rs16971832	0.83[ASN][1000 genomes]
rs16971834	0.84[ASN][1000 genomes]
rs1757455	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2015781	0.81[EUR][1000 genomes]
rs2777491	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28600680	0.92[EUR][1000 genomes]
rs28792672	0.88[EUR][1000 genomes]
rs316605	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs316609	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs316610	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs316613	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs316614	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs316615	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs316617	0.84[EUR][1000 genomes]
rs3743038	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59590312	0.88[EUR][1000 genomes]
rs66538814	0.92[EUR][1000 genomes]
rs7163788	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7167729	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7168177	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7177641	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7180492	0.81[ASN][1000 genomes]
rs7181911	0.91[EUR][1000 genomes]
rs7182667	0.90[EUR][1000 genomes]
rs7182700	0.90[EUR][1000 genomes]
rs8024774	0.80[EUR][1000 genomes]
rs8026197	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8027626	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8036527	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8037824	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs823716	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs919961	0.81[EUR][1000 genomes]
rs9972288	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv904110	chr15:41776692-41813279	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv904111	chr15:41777898-41805115	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1655556	NDUFAF1	cis	Thyroid	GTEx
rs1655556	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs1655556	NDUFAF1	cis	Muscle Skeletal	GTEx
rs1655556	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs1655556	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs1655556	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs1655556	OIP5-AS1	cis	Artery Tibial	GTEx
rs1655556	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs1655556	NDUFAF1	cis	multi-tissue	Pritchard
rs1655556	OIP5-AS1	cis	Nerve Tibial	GTEx
rs1655556	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41765600-41778400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:41769600-41779200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:41769600-41780200	Weak transcription	Right Atrium	heart
4	chr15:41771600-41780200	Weak transcription	Fetal Heart	heart
5	chr15:41773000-41779600	Weak transcription	HUVEC	blood vessel
6	chr15:41773200-41779200	Weak transcription	Hela-S3	cervix
7	chr15:41773400-41779600	Weak transcription	Colonic Mucosa	Colon
8	chr15:41773400-41785000	Weak transcription	A549	lung
9	chr15:41773600-41778200	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:41773800-41778600	Weak transcription	Aorta	Aorta
11	chr15:41773800-41780000	Weak transcription	HMEC	breast
12	chr15:41773800-41780200	Weak transcription	NHLF	lung
13	chr15:41773800-41784000	Weak transcription	HepG2	liver
14	chr15:41774000-41778800	Weak transcription	Spleen	Spleen
15	chr15:41774000-41779000	Weak transcription	Right Ventricle	heart
16	chr15:41774000-41779400	Weak transcription	Lung	lung
17	chr15:41774000-41782200	Weak transcription	Osteobl	bone
18	chr15:41774600-41779600	Weak transcription	NH-A	brain
19	chr15:41774800-41778000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:41774800-41784600	Weak transcription	Dnd41	blood
21	chr15:41775000-41779400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr15:41775000-41780400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:41775400-41778400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:41775400-41779000	Weak transcription	Adipose Nuclei	Adipose
25	chr15:41775400-41779600	Weak transcription	Fetal Kidney	kidney
26	chr15:41775400-41780000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:41775400-41780000	Weak transcription	Esophagus	oesophagus
28	chr15:41775400-41780000	Weak transcription	Fetal Thymus	thymus
29	chr15:41775400-41780400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr15:41775400-41784800	Weak transcription	Liver	Liver
31	chr15:41775600-41778200	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:41775600-41780000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr15:41775600-41781800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:41775600-41781800	Weak transcription	NHDF-Ad	bronchial
35	chr15:41775600-41782200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:41775600-41783800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr15:41775600-41784800	Weak transcription	Brain Angular Gyrus	brain
38	chr15:41775800-41778000	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:41775800-41778600	Weak transcription	Primary T cells from cord blood	blood
40	chr15:41775800-41778800	Weak transcription	Brain Anterior Caudate	brain
41	chr15:41775800-41780200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr15:41775800-41782200	Weak transcription	HSMMtube	muscle
43	chr15:41776000-41778800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:41776000-41779000	Weak transcription	Brain Substantia Nigra	brain
45	chr15:41776000-41779400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr15:41776000-41779600	Weak transcription	Gastric	stomach
47	chr15:41776000-41779800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:41776000-41780000	Weak transcription	Fetal Lung	lung
49	chr15:41776000-41780000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr15:41776000-41780000	Weak transcription	HSMM	muscle

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