Variant report

Variant	rs12101934
Chromosome Location	chr15:41353079-41353080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41352417..41354404-chr15:41357276..41359773,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1001341	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs1009913	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs11853192	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11854472	0.84[ASN][1000 genomes]
rs11855248	0.81[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs11855797	0.84[EUR][1000 genomes]
rs11856848	0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs11858115	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs11858678	0.95[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12324159	0.81[EUR][1000 genomes]
rs1659227	0.81[EUR][1000 genomes]
rs1678750	0.81[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs1717200	0.99[ASN][1000 genomes]
rs1869907	0.81[CHB][hapmap];0.98[GIH][hapmap]
rs1983400	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2164996	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs2306083	0.81[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs2578655	0.81[EUR][1000 genomes]
rs28409432	0.84[EUR][1000 genomes]
rs28473405	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs28510775	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28516683	0.84[EUR][1000 genomes]
rs28613002	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28688742	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28828670	0.82[EUR][1000 genomes]
rs2918462	0.86[MEX][hapmap];0.85[TSI][hapmap]
rs2925343	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs2925345	1.00[ASW][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs2927061	0.81[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs2927062	0.81[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs2928148	0.81[ASN][1000 genomes]
rs2928156	0.87[EUR][1000 genomes]
rs2947493	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2947494	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3100807	0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap]
rs3101436	0.81[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs3214068	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs36046988	0.81[EUR][1000 genomes]
rs3900905	0.80[CEU][hapmap];0.89[JPT][hapmap]
rs4592624	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs476633	0.91[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs516156	0.83[ASN][1000 genomes]
rs537244	0.81[EUR][1000 genomes]
rs544744	0.86[ASN][1000 genomes]
rs551482	0.81[EUR][1000 genomes]
rs561301	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61203391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492983	0.85[EUR][1000 genomes]
rs6492993	0.86[MEX][hapmap];0.85[TSI][hapmap]
rs6492997	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs66818965	0.81[ASN][1000 genomes]
rs690733	0.95[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs691672	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs691702	0.81[EUR][1000 genomes]
rs691830	0.97[ASN][1000 genomes]
rs692153	0.91[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs692195	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7169375	0.81[CHB][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs7170049	0.85[TSI][hapmap]
rs7173086	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs7173841	0.82[EUR][1000 genomes]
rs7180853	0.84[EUR][1000 genomes]
rs7181816	0.84[ASN][1000 genomes]
rs8027932	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8033435	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8037837	0.81[ASN][1000 genomes]
rs9888710	0.84[EUR][1000 genomes]
rs9888718	0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053462	chr15:41270067-41396094	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12101934	NDUFAF1	cis	lymphoblastoid	seeQTL
rs12101934	NDUFAF1	cis	parietal	SCAN
rs12101934	BUB1B	cis	parietal	SCAN
rs12101934	NDUFAF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41276600-41354600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:41325600-41354000	Strong transcription	Primary B cells from peripheral blood	blood
3	chr15:41325800-41354000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:41328400-41353200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr15:41328800-41388600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:41329800-41353400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:41330200-41353400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr15:41330200-41354000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:41330400-41354000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:41330400-41354400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr15:41330600-41353200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr15:41330600-41353600	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr15:41330800-41353200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:41330800-41353200	Strong transcription	Fetal Thymus	thymus
15	chr15:41330800-41353400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:41330800-41353600	Strong transcription	Placenta	Placenta
17	chr15:41330800-41354600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr15:41331000-41355600	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr15:41331200-41354000	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr15:41331200-41354000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:41332400-41355800	Strong transcription	Stomach Smooth Muscle	stomach
22	chr15:41332600-41355600	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:41334400-41353400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:41334600-41389000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr15:41335400-41358800	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:41336600-41353600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:41336600-41354000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:41336600-41354000	Strong transcription	Adipose Nuclei	Adipose
29	chr15:41336600-41354600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:41336800-41353200	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr15:41336800-41380400	Strong transcription	Osteobl	bone
32	chr15:41337000-41353800	Strong transcription	Left Ventricle	heart
33	chr15:41338600-41353200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:41339000-41353400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:41340800-41366800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr15:41341200-41355200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr15:41341600-41354600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr15:41341600-41360400	Weak transcription	Stomach Mucosa	stomach
39	chr15:41341600-41389000	Strong transcription	Liver	Liver
40	chr15:41341800-41353400	Strong transcription	Duodenum Mucosa	Duodenum
41	chr15:41341800-41356000	Strong transcription	HepG2	liver
42	chr15:41342000-41353400	Strong transcription	Fetal Intestine Large	intestine
43	chr15:41344400-41353600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:41344600-41353200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr15:41345200-41373600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr15:41345600-41353600	Strong transcription	Hela-S3	cervix
47	chr15:41345600-41354000	Strong transcription	HSMM	muscle
48	chr15:41346000-41353200	Strong transcription	NH-A	brain
49	chr15:41346000-41358000	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr15:41346600-41353400	Strong transcription	Fetal Intestine Small	intestine

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