Variant report

Variant	rs2925345
Chromosome Location	chr15:41311799-41311800
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41311750-41311840	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41234066..41235999-chr15:41310279..41312553,2	MCF-7	breast:
2	chr15:41309360..41312229-chr15:41317584..41319591,2	K562	blood:
3	chr15:41310991..41312633-chr15:41317212..41318935,2	MCF-7	breast:
4	chr15:41220351..41222994-chr15:41310028..41311889,2	K562	blood:
5	chr15:41305413..41309160-chr15:41310948..41312697,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000259521	TF binding region
ENSG00000259521	Chromatin interaction
ENSG00000128917	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1001341	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1009913	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11070315	1.00[CEU][hapmap]
rs11854472	0.84[EUR][1000 genomes]
rs11855248	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11856572	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11856577	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11856848	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11858678	0.82[MEX][hapmap]
rs12899590	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12905926	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12910027	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13329511	0.85[ASN][1000 genomes]
rs1678750	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs1717200	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1869907	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs1962410	0.82[EUR][1000 genomes]
rs2306083	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2412572	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2412574	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28473405	0.88[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs28479904	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28501589	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28572344	0.82[EUR][1000 genomes]
rs28581803	0.85[EUR][1000 genomes]
rs2899002	1.00[CEU][hapmap]
rs2925342	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2925343	0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2925346	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2927061	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2927062	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3100807	0.96[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3101436	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3214068	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3900905	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3986311	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4244584	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4497658	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs476633	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4923890	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4924525	0.82[EUR][1000 genomes]
rs4924532	0.84[EUR][1000 genomes]
rs516156	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs544744	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6492978	0.84[EUR][1000 genomes]
rs690733	0.82[MEX][hapmap]
rs691830	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs692153	0.80[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs692155	0.96[CEU][hapmap]
rs7162992	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7169375	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7171437	0.85[ASN][1000 genomes]
rs7179681	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7181816	0.84[EUR][1000 genomes]
rs72737704	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8030306	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8042088	0.85[EUR][1000 genomes]
rs9796	0.96[CEU][hapmap];0.81[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2925345	NDUFAF1	cis	parietal	SCAN
rs2925345	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs2925345	NDUFAF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41258800-41348400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:41276600-41354600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:41280400-41339800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:41294000-41313000	Weak transcription	Esophagus	oesophagus
5	chr15:41294000-41314600	Weak transcription	Aorta	Aorta
6	chr15:41294000-41316600	Weak transcription	Pancreas	Pancrea
7	chr15:41294200-41316800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:41296000-41315600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:41300200-41322400	Strong transcription	Primary T cells from cord blood	blood
10	chr15:41301600-41313800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr15:41301800-41315600	Strong transcription	Dnd41	blood
12	chr15:41302200-41315600	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr15:41302200-41315800	Strong transcription	K562	blood
14	chr15:41302800-41314000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:41303200-41314600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:41303200-41315000	Strong transcription	NHEK	skin
17	chr15:41303200-41320200	Strong transcription	Hela-S3	cervix
18	chr15:41303400-41313200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:41303400-41314200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr15:41303400-41321800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:41303400-41323400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:41303600-41318000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr15:41303800-41314000	Strong transcription	Fetal Muscle Leg	muscle
24	chr15:41304200-41318000	Weak transcription	Small Intestine	intestine
25	chr15:41304600-41315600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:41304800-41312200	Strong transcription	HSMM	muscle
27	chr15:41304800-41314800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:41304800-41322200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:41305000-41314800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr15:41305200-41313400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:41305800-41314800	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:41306000-41314200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:41306000-41322200	Strong transcription	Fetal Thymus	thymus
34	chr15:41306200-41313400	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr15:41306400-41315600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr15:41306600-41312800	Weak transcription	A549	lung
37	chr15:41306600-41314800	Strong transcription	HSMMtube	muscle
38	chr15:41306800-41313200	Strong transcription	NHDF-Ad	bronchial
39	chr15:41306800-41314200	Strong transcription	Primary B cells from cord blood	blood
40	chr15:41306800-41315200	Strong transcription	Left Ventricle	heart
41	chr15:41306800-41316400	Weak transcription	Fetal Heart	heart
42	chr15:41306800-41338800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr15:41307000-41313600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr15:41307600-41314000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr15:41307600-41314400	Strong transcription	Fetal Stomach	stomach
46	chr15:41307600-41335000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr15:41307800-41313200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr15:41307800-41313200	Strong transcription	Thymus	Thymus
49	chr15:41307800-41314800	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr15:41308200-41314800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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