Variant report

Variant	rs2164996
Chromosome Location	chr15:41536624-41536625
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	chr15:41521136..41528560-chr15:41530721..41537224,13	K562	blood:
2	chr15:41535934..41538302-chr15:41541101..41542958,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187446	Chromatin interaction
ENSG00000178997	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10152855	0.85[ASN][1000 genomes]
rs11855102	0.80[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11858115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858678	0.92[ASW][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs12324159	0.84[EUR][1000 genomes]
rs1659227	0.85[EUR][1000 genomes]
rs16971693	0.82[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs16971700	0.88[ASN][1000 genomes]
rs1717198	0.81[EUR][1000 genomes]
rs1866400	0.82[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1965139	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1965140	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1971131	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs2083239	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2578655	0.84[EUR][1000 genomes]
rs28409265	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493237	0.85[ASN][1000 genomes]
rs28495204	0.85[ASN][1000 genomes]
rs28568756	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28615543	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28665387	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28735224	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899013	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2918462	1.00[ASW][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs41442144	0.87[ASN][1000 genomes]
rs4258585	0.85[ASN][1000 genomes]
rs4419033	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4445868	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs494490	0.82[GIH][hapmap];0.85[TSI][hapmap]
rs537244	0.85[EUR][1000 genomes]
rs551482	0.85[EUR][1000 genomes]
rs55756301	0.83[ASN][1000 genomes]
rs56082289	0.83[ASN][1000 genomes]
rs59389433	0.83[ASN][1000 genomes]
rs59691280	0.83[ASN][1000 genomes]
rs6492991	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6492992	0.82[ASN][1000 genomes]
rs6492993	0.92[ASW][hapmap];0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6492994	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6492997	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492998	0.85[TSI][hapmap]
rs690733	0.92[ASW][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs691702	0.85[EUR][1000 genomes]
rs692153	0.82[CHD][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs7162443	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7162503	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166205	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7166905	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7167813	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170049	0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs7173086	1.00[ASW][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7175912	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7178840	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7179231	0.82[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7179969	0.82[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs8026858	0.81[CHB][hapmap]
rs8032589	0.80[JPT][hapmap]
rs8035252	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs8036602	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8038834	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs8039014	0.82[CHB][hapmap]
rs8039915	0.83[ASN][1000 genomes]
rs8039934	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs8043253	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs909023	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs909024	0.85[ASN][1000 genomes]
rs909025	0.90[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs9972349	0.88[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9972622	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9972623	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457120	chr15:41410705-41546631	Strong transcription Weak transcription Enhancers Flanking Active TSS 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	17 gene(s)	inside rSNPs	diseases
2	nsv569231	chr15:41410705-41546631	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv1844058	chr15:41511916-41548948	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2164996	TTBK2	cis	cerebellum	SCAN
rs2164996	BUB1B	cis	parietal	SCAN
rs2164996	NDUFAF1	cis	Muscle Skeletal	GTEx
rs2164996	GPR176	cis	parietal	SCAN
rs2164996	NDUFAF1	cis	cerebellum	SCAN
rs2164996	NDUFAF1	cis	Thyroid	GTEx
rs2164996	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs2164996	NUSAP1	cis	cerebellum	SCAN
rs2164996	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs2164996	NDUFAF1	cis	parietal	SCAN
rs2164996	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs2164996	NDUFAF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41524200-41546200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr15:41524200-41554800	Weak transcription	Fetal Thymus	thymus
3	chr15:41524200-41555800	Weak transcription	Aorta	Aorta
4	chr15:41524200-41563800	Weak transcription	Small Intestine	intestine
5	chr15:41524200-41575800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:41524400-41555800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:41524800-41546200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:41524800-41563800	Weak transcription	Esophagus	oesophagus
9	chr15:41525000-41548400	Weak transcription	Fetal Lung	lung
10	chr15:41525200-41548200	Weak transcription	Fetal Kidney	kidney
11	chr15:41525200-41554200	Weak transcription	Fetal Brain Female	brain
12	chr15:41525200-41556400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:41525200-41575400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr15:41525400-41538800	Weak transcription	Fetal Muscle Leg	muscle
15	chr15:41525400-41556200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr15:41525400-41556800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr15:41525800-41554800	Weak transcription	Dnd41	blood
18	chr15:41525800-41575200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr15:41526000-41541800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:41526000-41554800	Weak transcription	Brain Angular Gyrus	brain
21	chr15:41526200-41542200	Weak transcription	NH-A	brain
22	chr15:41526200-41554800	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:41526400-41542200	Weak transcription	HSMMtube	muscle
24	chr15:41532000-41542000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:41532400-41550600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr15:41533200-41539600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:41533200-41548400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:41533200-41552400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:41533400-41537400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr15:41533800-41538600	Strong transcription	Hela-S3	cervix
31	chr15:41533800-41554600	Weak transcription	Brain Anterior Caudate	brain
32	chr15:41533800-41555000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr15:41534000-41536800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr15:41534000-41538600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:41534000-41538800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:41534000-41538800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr15:41534000-41541200	Weak transcription	Thymus	Thymus
38	chr15:41534000-41542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:41534000-41543200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:41534000-41555200	Weak transcription	Brain Germinal Matrix	brain
41	chr15:41534200-41537000	Weak transcription	Psoas Muscle	Psoas
42	chr15:41534200-41551000	Weak transcription	GM12878-XiMat	blood
43	chr15:41534200-41555200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:41534200-41556400	Weak transcription	Spleen	Spleen
45	chr15:41534400-41536800	Weak transcription	A549	lung
46	chr15:41534400-41537000	Weak transcription	Osteobl	bone
47	chr15:41534400-41544600	Weak transcription	HSMM	muscle
48	chr15:41534600-41536800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr15:41534600-41537800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr15:41534800-41540400	Weak transcription	Stomach Mucosa	stomach

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