Variant report

Variant	rs3794537
Chromosome Location	chr15:52099158-52099159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52098121..52099949-chr15:52102548..52104205,2	K562	blood:
2	chr15:52097471..52100058-chr15:52117119..52119729,2	MCF-7	breast:
3	chr15:52098625..52100284-chr15:52119574..52122353,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1025185	1.00[EUR][1000 genomes]
rs10519323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10519325	1.00[EUR][1000 genomes]
rs10519326	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12438469	1.00[EUR][1000 genomes]
rs12442283	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1378891	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1426085	1.00[EUR][1000 genomes]
rs1426086	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16964523	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17649047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17649178	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17649208	1.00[JPT][hapmap]
rs17649255	0.86[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17649391	1.00[EUR][1000 genomes]
rs17649692	1.00[EUR][1000 genomes]
rs17649801	1.00[EUR][1000 genomes]
rs17705530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17705649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17705685	1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17705889	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17706076	1.00[EUR][1000 genomes]
rs2052707	1.00[EUR][1000 genomes]
rs2162224	1.00[EUR][1000 genomes]
rs2414118	0.88[AMR][1000 genomes]
rs2436664	1.00[EUR][1000 genomes]
rs2470613	1.00[EUR][1000 genomes]
rs2554309	1.00[EUR][1000 genomes]
rs2554310	1.00[EUR][1000 genomes]
rs2554311	1.00[EUR][1000 genomes]
rs2554318	1.00[EUR][1000 genomes]
rs2554323	1.00[EUR][1000 genomes]
rs2554325	1.00[EUR][1000 genomes]
rs2554326	1.00[EUR][1000 genomes]
rs2554330	1.00[EUR][1000 genomes]
rs2554333	1.00[EUR][1000 genomes]
rs2554351	1.00[EUR][1000 genomes]
rs2554352	1.00[EUR][1000 genomes]
rs2554356	1.00[EUR][1000 genomes]
rs2570218	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2570219	1.00[EUR][1000 genomes]
rs2570220	1.00[EUR][1000 genomes]
rs2570221	1.00[EUR][1000 genomes]
rs2570227	1.00[EUR][1000 genomes]
rs2570242	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2570244	1.00[EUR][1000 genomes]
rs2570245	1.00[EUR][1000 genomes]
rs2570247	1.00[EUR][1000 genomes]
rs2570249	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2570250	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2570256	1.00[EUR][1000 genomes]
rs2570257	1.00[EUR][1000 genomes]
rs2570259	1.00[EUR][1000 genomes]
rs2570261	1.00[EUR][1000 genomes]
rs2570267	1.00[EUR][1000 genomes]
rs2570270	1.00[EUR][1000 genomes]
rs2570273	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2570274	1.00[EUR][1000 genomes]
rs2593165	1.00[EUR][1000 genomes]
rs2593175	1.00[EUR][1000 genomes]
rs2593176	1.00[EUR][1000 genomes]
rs2593180	1.00[EUR][1000 genomes]
rs2623246	1.00[EUR][1000 genomes]
rs2623250	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2623252	1.00[EUR][1000 genomes]
rs2623257	1.00[EUR][1000 genomes]
rs2623260	1.00[EUR][1000 genomes]
rs2623264	1.00[EUR][1000 genomes]
rs2623267	1.00[EUR][1000 genomes]
rs2623268	1.00[EUR][1000 genomes]
rs2623269	1.00[EUR][1000 genomes]
rs2623277	1.00[EUR][1000 genomes]
rs2623278	1.00[EUR][1000 genomes]
rs2623287	1.00[EUR][1000 genomes]
rs2899483	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2916174	1.00[EUR][1000 genomes]
rs2959297	1.00[EUR][1000 genomes]
rs2959303	1.00[EUR][1000 genomes]
rs3099570	1.00[EUR][1000 genomes]
rs34407523	1.00[EUR][1000 genomes]
rs36097346	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3794533	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774600	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4774601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4775971	0.91[AMR][1000 genomes]
rs4775979	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4775987	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4775988	1.00[EUR][1000 genomes]
rs4775989	1.00[EUR][1000 genomes]
rs7166322	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7166954	0.83[AMR][1000 genomes]
rs7170429	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7170700	1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7173661	1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7179139	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72730966	0.84[ASN][1000 genomes]
rs73407386	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73407396	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73409011	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73411105	1.00[EUR][1000 genomes]
rs8024441	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8026507	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8027426	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8042310	1.00[EUR][1000 genomes]
rs919057	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs990666	0.86[JPT][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv3361968	chr15:52087428-52107237	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52052200-52101800	Weak transcription	Colonic Mucosa	Colon
2	chr15:52052600-52106600	Weak transcription	HSMM	muscle
3	chr15:52060200-52103400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:52060800-52101200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:52060800-52102600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:52060800-52105400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:52061600-52112000	Weak transcription	NHLF	lung
8	chr15:52074000-52100000	Weak transcription	NHDF-Ad	bronchial
9	chr15:52074800-52102800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:52076800-52104400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:52080800-52102600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:52085800-52105200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:52085800-52108800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr15:52089000-52106400	Weak transcription	HSMMtube	muscle
15	chr15:52089200-52107200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr15:52089400-52099200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr15:52089600-52101200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr15:52089800-52101000	Weak transcription	Fetal Intestine Small	intestine
19	chr15:52090400-52104400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr15:52091200-52104600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:52091200-52109400	Weak transcription	Gastric	stomach
22	chr15:52091400-52099400	Weak transcription	Pancreas	Pancrea
23	chr15:52091400-52103600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr15:52091800-52108200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:52092000-52107800	Weak transcription	Fetal Muscle Leg	muscle
26	chr15:52092200-52101200	Weak transcription	Dnd41	blood
27	chr15:52093400-52101800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:52093600-52105200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr15:52093800-52108600	Weak transcription	Fetal Lung	lung
30	chr15:52095000-52101800	Weak transcription	Psoas Muscle	Psoas
31	chr15:52095800-52101800	Strong transcription	Brain Hippocampus Middle	brain
32	chr15:52096000-52104800	Weak transcription	Placenta	Placenta
33	chr15:52097000-52100000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr15:52097200-52103000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr15:52097600-52102000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr15:52098200-52099200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:52098200-52099400	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr15:52098200-52099600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr15:52098200-52099800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr15:52098200-52100000	Strong transcription	Fetal Stomach	stomach
41	chr15:52098200-52100800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr15:52098200-52101400	Strong transcription	Brain Germinal Matrix	brain
43	chr15:52098200-52102000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:52098400-52099400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:52098400-52099800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:52098400-52099800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:52098400-52099800	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr15:52098400-52099800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:52098400-52099800	Strong transcription	Aorta	Aorta
50	chr15:52098400-52099800	Strong transcription	Brain Substantia Nigra	brain

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