Variant report

Variant	rs933858
Chromosome Location	chr15:52934402-52934403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52934298..52936704-chr15:52937679..52940087,2	MCF-7	breast:
2	chr15:52924022..52926250-chr15:52933735..52936192,2	MCF-7	breast:
3	chr15:52927735..52930583-chr15:52932709..52935463,2	K562	blood:
4	chr15:52932870..52937961-chr15:52968619..52973908,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000047346	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10775148	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10775149	0.87[CEU][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070904	1.00[CEU][hapmap]
rs11070910	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11629479	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11634879	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12102061	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12900462	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12908944	0.88[EUR][1000 genomes]
rs12916276	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12916405	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2414162	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2414165	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2414168	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414169	1.00[CEU][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414170	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2414171	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2414174	1.00[CEU][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2414176	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414177	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28402931	0.82[AFR][1000 genomes]
rs2899493	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34340005	0.82[EUR][1000 genomes]
rs35756938	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35760898	0.94[EUR][1000 genomes]
rs4386077	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4404000	1.00[CEU][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4774635	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4776064	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62025584	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62025586	0.97[EUR][1000 genomes]
rs6493570	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7162184	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7166478	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7168045	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7169849	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7179310	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs8026304	0.83[AMR][1000 genomes]
rs8026469	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8032889	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8035115	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8036671	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8036680	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8040787	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8042646	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs933859	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9806267	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[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:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52861800-52934800	Weak transcription	Right Ventricle	heart
2	chr15:52869400-52945400	Weak transcription	Small Intestine	intestine
3	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr15:52874800-52944200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:52885600-52945200	Weak transcription	Spleen	Spleen
6	chr15:52899600-52944400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr15:52900600-52944000	Strong transcription	Primary B cells from peripheral blood	blood
8	chr15:52900800-52945200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr15:52902200-52943800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:52902400-52934800	Weak transcription	NH-A	brain
11	chr15:52902600-52942000	Weak transcription	HUVEC	blood vessel
12	chr15:52903400-52943800	Weak transcription	Hela-S3	cervix
13	chr15:52903400-52944000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:52903600-52942400	Weak transcription	Dnd41	blood
15	chr15:52903600-52945400	Weak transcription	Colonic Mucosa	Colon
16	chr15:52904000-52943400	Weak transcription	Fetal Kidney	kidney
17	chr15:52904000-52945400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:52904000-52956800	Weak transcription	Esophagus	oesophagus
19	chr15:52906200-52944000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr15:52908600-52956200	Weak transcription	Gastric	stomach
21	chr15:52909000-52942400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:52909600-52944000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:52909600-52950800	Weak transcription	Pancreas	Pancrea
24	chr15:52915600-52944200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr15:52915800-52938400	Weak transcription	Ovary	ovary
26	chr15:52916200-52934800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr15:52916200-52942800	Weak transcription	Fetal Brain Female	brain
28	chr15:52916800-52934800	Weak transcription	Brain Substantia Nigra	brain
29	chr15:52916800-52936000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr15:52917000-52938400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr15:52917000-52943600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:52920800-52942800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr15:52921800-52939400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr15:52921800-52939600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:52923200-52945200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr15:52925800-52935000	Weak transcription	Psoas Muscle	Psoas
37	chr15:52925800-52935400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:52927000-52938200	Weak transcription	Fetal Intestine Large	intestine
39	chr15:52927800-52939800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:52927800-52943800	Weak transcription	Fetal Muscle Leg	muscle
41	chr15:52927800-52947600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr15:52927800-52958600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:52928000-52942400	Weak transcription	Brain Germinal Matrix	brain
44	chr15:52928000-52944000	Weak transcription	Fetal Intestine Small	intestine
45	chr15:52928000-52955200	Weak transcription	Thymus	Thymus
46	chr15:52928000-52956400	Weak transcription	Lung	lung
47	chr15:52928200-52943800	Weak transcription	Fetal Stomach	stomach
48	chr15:52928200-52945400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:52929200-52934800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:52929200-52942800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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