Variant report

Variant	rs12900462
Chromosome Location	chr15:52950606-52950607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:52950435..52952896-chr15:52954166..52957098,2	K562	blood:
2	chr15:52938830..52941710-chr15:52949842..52951854,2	MCF-7	breast:
3	chr15:52942408..52952117-chr15:52965431..52973600,32	MCF-7	breast:
4	chr15:52950435..52952997-chr15:52969814..52971344,2	K562	blood:
5	chr15:52860334..52861897-chr15:52949806..52952761,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARPP19-2	chr15:52950327-52950994	NONHSAT043941

No data

Variant related genes	Relation type
ENSG00000128989	Chromatin interaction
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	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10775149	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs11070904	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11070910	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11629479	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11634879	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs12102061	0.91[EUR][1000 genomes]
rs12908944	0.82[EUR][1000 genomes]
rs12916276	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12916405	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2414162	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2414164	0.95[TSI][hapmap]
rs2414165	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2414168	0.94[EUR][1000 genomes]
rs2414169	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2414170	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2414171	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2414174	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2414176	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2414177	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2899493	0.98[EUR][1000 genomes]
rs34340005	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35756938	0.91[EUR][1000 genomes]
rs35760898	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4386077	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs4404000	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4774635	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4776064	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs62025584	0.94[EUR][1000 genomes]
rs62025586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6493570	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7162184	0.88[EUR][1000 genomes]
rs7166478	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7168045	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7169849	0.89[EUR][1000 genomes]
rs7179310	1.00[CEU][hapmap]
rs8026469	0.85[EUR][1000 genomes]
rs8032889	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs8035115	0.98[EUR][1000 genomes]
rs8036671	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8036680	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8040787	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs8042646	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs933858	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs933859	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9806267	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.87[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:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr15:52904000-52956800	Weak transcription	Esophagus	oesophagus
3	chr15:52908600-52956200	Weak transcription	Gastric	stomach
4	chr15:52909600-52950800	Weak transcription	Pancreas	Pancrea
5	chr15:52927800-52958600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:52928000-52955200	Weak transcription	Thymus	Thymus
7	chr15:52928000-52956400	Weak transcription	Lung	lung
8	chr15:52944200-52951800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr15:52944200-52965800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:52944400-52951000	Weak transcription	Fetal Stomach	stomach
11	chr15:52944400-52957000	Weak transcription	Brain Germinal Matrix	brain
12	chr15:52944400-52969600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:52944400-52970200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:52944600-52962000	Weak transcription	Aorta	Aorta
15	chr15:52944600-52965000	Strong transcription	Primary B cells from cord blood	blood
16	chr15:52944600-52965400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr15:52944600-52969800	Weak transcription	Fetal Brain Male	brain
18	chr15:52944800-52951000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr15:52944800-52952000	Strong transcription	Primary hematopoietic stem cells	blood
20	chr15:52945000-52965400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:52945000-52968600	Weak transcription	HepG2	liver
22	chr15:52945200-52959800	Weak transcription	Dnd41	blood
23	chr15:52945400-52951200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:52945400-52951600	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr15:52945400-52956600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:52945400-52965400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr15:52945600-52950800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:52945600-52956200	Weak transcription	Colonic Mucosa	Colon
29	chr15:52945600-52958400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr15:52945600-52962800	Strong transcription	Placenta	Placenta
31	chr15:52945800-52950800	Weak transcription	Fetal Muscle Leg	muscle
32	chr15:52945800-52951000	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:52945800-52951000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr15:52945800-52951000	Weak transcription	Fetal Intestine Small	intestine
35	chr15:52945800-52951400	Strong transcription	Primary T cells from cord blood	blood
36	chr15:52945800-52951400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr15:52945800-52956800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:52946000-52950800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:52946000-52950800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr15:52946000-52950800	Weak transcription	Left Ventricle	heart
41	chr15:52946000-52951000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:52946000-52951000	Weak transcription	Psoas Muscle	Psoas
43	chr15:52946000-52956800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr15:52946000-52956800	Weak transcription	Small Intestine	intestine
45	chr15:52946000-52962000	Weak transcription	Right Ventricle	heart
46	chr15:52946000-52962000	Weak transcription	Spleen	Spleen
47	chr15:52946000-52965200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr15:52946000-52968200	Weak transcription	Fetal Heart	heart
49	chr15:52946000-52968600	Weak transcription	Stomach Mucosa	stomach
50	chr15:52946200-52951000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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