Variant report

Variant	rs2414170
Chromosome Location	chr15:52943241-52943242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr15:52941897-52945775	SK-N-SH	brain:	n/a	chr15:52944270-52944284
2	RFX5	chr15:52943036-52943316	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52942408..52952117-chr15:52965431..52973600,32	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259935	TF binding region
ENSG00000047346	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10775148	0.90[EUR][1000 genomes]
rs10775149	0.87[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11070904	1.00[CEU][hapmap]
rs11070910	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11629479	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11634879	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12102061	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12900462	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs12908944	0.85[EUR][1000 genomes]
rs12916276	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12916405	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2414162	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2414165	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2414168	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2414169	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2414171	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414174	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2414176	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2414177	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2899493	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34340005	0.85[EUR][1000 genomes]
rs35756938	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35760898	0.90[EUR][1000 genomes]
rs4386077	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4404000	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4774635	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4776064	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62025584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62025586	1.00[EUR][1000 genomes]
rs6493570	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7162184	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7166478	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7168045	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7169849	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7179310	1.00[CEU][hapmap]
rs8026304	0.81[AMR][1000 genomes]
rs8026469	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8032889	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8035115	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8036671	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8036680	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8040787	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8042646	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs933858	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs933859	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9806267	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv457140	chr15:52901433-52968746	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52869400-52945400	Weak transcription	Small Intestine	intestine
2	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr15:52874800-52944200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:52885600-52945200	Weak transcription	Spleen	Spleen
5	chr15:52899600-52944400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr15:52900600-52944000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr15:52900800-52945200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr15:52902200-52943800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:52903400-52943800	Weak transcription	Hela-S3	cervix
10	chr15:52903400-52944000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:52903600-52945400	Weak transcription	Colonic Mucosa	Colon
12	chr15:52904000-52943400	Weak transcription	Fetal Kidney	kidney
13	chr15:52904000-52945400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:52904000-52956800	Weak transcription	Esophagus	oesophagus
15	chr15:52906200-52944000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:52908600-52956200	Weak transcription	Gastric	stomach
17	chr15:52909600-52944000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:52909600-52950800	Weak transcription	Pancreas	Pancrea
19	chr15:52915600-52944200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:52917000-52943600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:52923200-52945200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr15:52927800-52943800	Weak transcription	Fetal Muscle Leg	muscle
23	chr15:52927800-52947600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr15:52927800-52958600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:52928000-52944000	Weak transcription	Fetal Intestine Small	intestine
26	chr15:52928000-52955200	Weak transcription	Thymus	Thymus
27	chr15:52928000-52956400	Weak transcription	Lung	lung
28	chr15:52928200-52943800	Weak transcription	Fetal Stomach	stomach
29	chr15:52928200-52945400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:52929400-52945200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:52929800-52944000	Weak transcription	Aorta	Aorta
32	chr15:52929800-52945200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr15:52930400-52943800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:52931000-52944000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:52934400-52943800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:52935000-52943600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr15:52935200-52943400	Weak transcription	HSMM	muscle
38	chr15:52935200-52943600	Weak transcription	Right Atrium	heart
39	chr15:52935200-52943800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr15:52935400-52943400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:52935400-52943600	Weak transcription	HMEC	breast
42	chr15:52935400-52943800	Weak transcription	Brain Substantia Nigra	brain
43	chr15:52935400-52944000	Weak transcription	Left Ventricle	heart
44	chr15:52935600-52943400	Weak transcription	GM12878-XiMat	blood
45	chr15:52935600-52943600	Weak transcription	NHDF-Ad	bronchial
46	chr15:52935800-52943400	Weak transcription	Osteobl	bone
47	chr15:52935800-52943800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:52935800-52944000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:52936000-52943400	Weak transcription	NHLF	lung
50	chr15:52936600-52943800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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