Variant report

Variant	rs16964523
Chromosome Location	chr15:52089700-52089701
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52088548..52091371-chr15:52091695..52094863,3	K562	blood:
2	chr15:52087845..52094257-chr15:52120068..52124048,9	MCF-7	breast:
3	chr15:52087804..52093803-chr15:52117139..52123482,14	MCF-7	breast:
4	chr15:52089220..52092399-chr15:52092458..52095936,3	K562	blood:
5	chr15:52089329..52092071-chr15:52108088..52110534,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10519323	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10519325	0.86[JPT][hapmap]
rs10519326	0.86[JPT][hapmap]
rs1426086	0.86[JPT][hapmap]
rs17649047	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs17649178	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17649208	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17649255	0.89[CHD][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap]
rs17649391	0.86[JPT][hapmap]
rs17649692	0.86[JPT][hapmap]
rs17705530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17705649	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17705685	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17705889	0.86[JPT][hapmap]
rs17706076	0.86[JPT][hapmap]
rs2052707	0.86[JPT][hapmap]
rs2162224	0.82[JPT][hapmap]
rs2436664	0.86[JPT][hapmap]
rs2554309	0.86[JPT][hapmap]
rs2554310	0.86[JPT][hapmap]
rs2554321	0.82[MEX][hapmap];1.00[TSI][hapmap]
rs2554333	0.86[JPT][hapmap]
rs2554341	0.82[MEX][hapmap];1.00[TSI][hapmap]
rs2554352	0.86[JPT][hapmap]
rs2554356	0.86[JPT][hapmap]
rs2570218	0.86[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs2570232	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap]
rs2570234	1.00[EUR][1000 genomes]
rs2570242	0.89[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs2570244	0.86[JPT][hapmap]
rs2570245	0.86[JPT][hapmap]
rs2570249	0.88[CHD][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap]
rs2570250	0.89[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs2570256	0.86[JPT][hapmap]
rs2570257	0.86[JPT][hapmap]
rs2570267	0.86[JPT][hapmap]
rs2570270	0.86[JPT][hapmap]
rs2570273	0.86[JPT][hapmap];1.00[TSI][hapmap]
rs2593175	0.86[JPT][hapmap]
rs2623246	0.86[JPT][hapmap]
rs2623248	0.86[JPT][hapmap]
rs2623250	0.89[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs2623253	1.00[EUR][1000 genomes]
rs2623256	0.81[AMR][1000 genomes]
rs2623264	0.86[JPT][hapmap]
rs2623269	0.86[JPT][hapmap]
rs2623277	0.86[JPT][hapmap]
rs2623287	0.86[JPT][hapmap]
rs2899483	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs36097346	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3794533	0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3794537	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4774601	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4775971	0.81[CHD][hapmap];0.82[AMR][1000 genomes]
rs4775979	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4775988	0.86[JPT][hapmap]
rs7166322	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7170429	1.00[JPT][hapmap]
rs7170700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7173661	1.00[CHD][hapmap];1.00[TSI][hapmap]
rs7179139	0.80[ASN][1000 genomes]
rs73407386	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73407396	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73409011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8024441	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8026507	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8027426	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs8042915	0.80[AMR][1000 genomes]
rs919056	0.86[JPT][hapmap]
rs919057	0.86[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs990666	0.86[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]

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:94 , 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	chr15:52053400-52090600	Weak transcription	Pancreas	Pancrea
4	chr15:52060200-52103400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:52060600-52091000	Weak transcription	Right Ventricle	heart
6	chr15:52060800-52101200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr15:52060800-52102600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:52060800-52105400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr15:52061600-52112000	Weak transcription	NHLF	lung
10	chr15:52061800-52098600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:52064400-52090400	Weak transcription	Left Ventricle	heart
12	chr15:52065600-52090600	Weak transcription	Spleen	Spleen
13	chr15:52065800-52091000	Weak transcription	Esophagus	oesophagus
14	chr15:52067200-52090600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr15:52067600-52090600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:52069200-52091000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:52074000-52090600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:52074000-52100000	Weak transcription	NHDF-Ad	bronchial
19	chr15:52074800-52102800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr15:52075000-52090600	Weak transcription	Dnd41	blood
21	chr15:52076400-52098400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr15:52076600-52090400	Weak transcription	Primary B cells from cord blood	blood
23	chr15:52076600-52090400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr15:52076600-52090400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr15:52076600-52090400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr15:52076600-52090600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr15:52076600-52090600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr15:52076800-52090800	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr15:52076800-52090800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr15:52076800-52104400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr15:52077000-52090400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:52077200-52098600	Weak transcription	Fetal Brain Male	brain
33	chr15:52079000-52098400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:52079200-52090600	Weak transcription	Fetal Thymus	thymus
35	chr15:52079200-52098600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:52079400-52090600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr15:52079600-52090400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:52080000-52090600	Weak transcription	Brain Anterior Caudate	brain
39	chr15:52080000-52090600	Weak transcription	Ovary	ovary
40	chr15:52080000-52099000	Weak transcription	Colon Smooth Muscle	Colon
41	chr15:52080200-52090400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr15:52080200-52090400	Weak transcription	Fetal Muscle Leg	muscle
43	chr15:52080200-52090600	Weak transcription	Fetal Stomach	stomach
44	chr15:52080400-52090400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:52080400-52090400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr15:52080400-52090400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:52080400-52090400	Weak transcription	Brain Angular Gyrus	brain
48	chr15:52080400-52090400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:52080400-52090600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:52080400-52090800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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