Variant report

Variant	rs2118740
Chromosome Location	chr15:41577232-41577233
allele	A/C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41522897..41527944-chr15:41573906..41578128,9	K562	blood:
2	chr15:41573497..41577986-chr15:41624362..41627823,9	K562	blood:
3	chr15:41575391..41577503-chr15:41623750..41625308,2	MCF-7	breast:
4	chr15:41576500..41578232-chr15:41585051..41586799,2	K562	blood:
5	chr15:41407604..41409854-chr15:41574990..41577590,2	K562	blood:
6	chr15:41574856..41577423-chr15:41692996..41695992,2	K562	blood:
7	chr15:41522629..41527275-chr15:41575215..41577611,6	K562	blood:
8	chr15:41575029..41577348-chr15:41624329..41626974,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137804	Chromatin interaction
ENSG00000128908	Chromatin interaction
ENSG00000104147	Chromatin interaction
ENSG00000187446	Chromatin interaction
ENSG00000137806	Chromatin interaction
ENSG00000178997	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10518717	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851403	1.00[ASN][1000 genomes]
rs11070328	0.87[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629979	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630799	1.00[ASN][1000 genomes]
rs11635269	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635565	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635906	1.00[ASN][1000 genomes]
rs11854081	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854632	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11854820	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11858068	1.00[ASN][1000 genomes]
rs11858812	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13313520	0.87[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329235	1.00[ASN][1000 genomes]
rs13329579	1.00[ASN][1000 genomes]
rs16971726	1.00[CHB][hapmap]
rs1757468	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17730589	0.94[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730888	0.87[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866399	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2448402	1.00[ASN][1000 genomes]
rs2730056	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2730058	1.00[ASN][1000 genomes]
rs28374715	1.00[CHB][hapmap]
rs28377562	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382348	1.00[ASN][1000 genomes]
rs28416360	1.00[ASN][1000 genomes]
rs28421136	1.00[ASN][1000 genomes]
rs28437576	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448670	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28456082	1.00[ASN][1000 genomes]
rs28458941	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28459164	0.83[AFR][1000 genomes]
rs28463309	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs28477406	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492932	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493087	1.00[ASN][1000 genomes]
rs28493702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535540	1.00[ASN][1000 genomes]
rs28554139	1.00[CHB][hapmap]
rs28555198	1.00[ASN][1000 genomes]
rs28557159	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs28576457	1.00[ASN][1000 genomes]
rs28584379	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28617619	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28623183	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661013	1.00[ASN][1000 genomes]
rs28663426	1.00[ASN][1000 genomes]
rs28673484	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28687846	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28700583	1.00[ASN][1000 genomes]
rs28703570	1.00[ASN][1000 genomes]
rs28712264	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716689	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28827035	1.00[ASN][1000 genomes]
rs28897479	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs316604	0.81[CEU][hapmap];1.00[ASN][1000 genomes]
rs316606	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs316607	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs316611	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs316616	1.00[ASN][1000 genomes]
rs3204853	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34040639	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs34665396	1.00[ASN][1000 genomes]
rs513280	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs521890	1.00[ASN][1000 genomes]
rs522063	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55725658	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56341337	0.84[EUR][1000 genomes]
rs56400990	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59000092	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493000	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493003	1.00[ASN][1000 genomes]
rs691011	1.00[ASN][1000 genomes]
rs691906	1.00[ASN][1000 genomes]
rs691907	1.00[ASN][1000 genomes]
rs7162231	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163989	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164211	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7164684	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7165396	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165914	0.87[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167706	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168002	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7168307	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168431	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7169543	0.87[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181982	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182324	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737786	1.00[ASN][1000 genomes]
rs72737792	1.00[ASN][1000 genomes]
rs72737793	1.00[ASN][1000 genomes]
rs72739630	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739644	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8023530	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8030228	0.81[EUR][1000 genomes]
rs8034840	1.00[ASN][1000 genomes]
rs8036026	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036734	1.00[ASN][1000 genomes]
rs8037574	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038132	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038983	1.00[ASN][1000 genomes]
rs8041809	1.00[ASN][1000 genomes]
rs8043237	1.00[ASN][1000 genomes]
rs9568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045455	chr15:41536624-41620534	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1044438	chr15:41560160-41745480	Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2118740	NDUFAF1	cis	Muscle Skeletal	GTEx
rs2118740	NDUFAF1	cis	Thyroid	GTEx
rs2118740	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs2118740	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs2118740	KRTAP4-7	cis	uninvolved skin	skin_eQTL
rs2118740	NDUFAF1	cis	multi-tissue	Pritchard
rs2118740	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs2118740	KRTAP4-7	cis	lesional skin	skin_eQTL
rs2118740	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs2118740	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs2118740	OIP5-AS1	cis	Artery Tibial	GTEx
rs2118740	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs2118740	KRTAP4-7	cis	normal skin	skin_eQTL
rs2118740	OIP5-AS1	cis	Nerve Tibial	GTEx
rs2118740	NDUFAF1	cis	lung	GTEx
rs2118740	OIP5-AS1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41575200-41577800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr15:41575400-41577400	Active TSS	Brain Angular Gyrus	brain
3	chr15:41575400-41577400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:41575400-41577400	Active TSS	Fetal Stomach	stomach
5	chr15:41575400-41577400	Active TSS	HSMM	muscle
6	chr15:41575400-41577600	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr15:41575400-41577600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:41575400-41577600	Active TSS	Brain Hippocampus Middle	brain
9	chr15:41575400-41577600	Active TSS	Psoas Muscle	Psoas
10	chr15:41575400-41577600	Active TSS	Stomach Smooth Muscle	stomach
11	chr15:41575400-41577800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:41575400-41577800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr15:41575400-41578400	Active TSS	Fetal Brain Female	brain
14	chr15:41575600-41577400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:41575600-41577400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr15:41575600-41577400	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr15:41575600-41577400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:41575600-41577400	Active TSS	Brain Cingulate Gyrus	brain
19	chr15:41575600-41577400	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr15:41575600-41577400	Active TSS	Colon Smooth Muscle	Colon
21	chr15:41575600-41577400	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr15:41575600-41577400	Active TSS	Fetal Lung	lung
23	chr15:41575600-41577400	Active TSS	Left Ventricle	heart
24	chr15:41575600-41577400	Active TSS	Pancreas	Pancrea
25	chr15:41575600-41577400	Active TSS	Right Ventricle	heart
26	chr15:41575600-41577600	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr15:41575600-41577600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:41575600-41577600	Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr15:41575600-41577800	Active TSS	H1 Cell Line	embryonic stem cell
30	chr15:41575600-41577800	Active TSS	H9 Cell Line	embryonic stem cell
31	chr15:41575600-41577800	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr15:41575600-41577800	Active TSS	Fetal Kidney	kidney
33	chr15:41575600-41577800	Active TSS	Ovary	ovary
34	chr15:41575600-41577800	Active TSS	GM12878-XiMat	blood
35	chr15:41575600-41578000	Active TSS	Brain Germinal Matrix	brain
36	chr15:41575600-41578000	Active TSS	Fetal Heart	heart
37	chr15:41575600-41578000	Active TSS	Right Atrium	heart
38	chr15:41575800-41577400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr15:41575800-41577400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:41575800-41577400	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr15:41575800-41577400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:41575800-41577400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr15:41575800-41577400	Active TSS	Fetal Brain Male	brain
44	chr15:41575800-41577400	Active TSS	Fetal Intestine Large	intestine
45	chr15:41575800-41577400	Active TSS	Fetal Muscle Trunk	muscle
46	chr15:41575800-41577400	Active TSS	Fetal Muscle Leg	muscle
47	chr15:41575800-41577400	Active TSS	Placenta	Placenta
48	chr15:41575800-41577400	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr15:41575800-41577400	Active TSS	Stomach Mucosa	stomach
50	chr15:41575800-41577600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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