Variant report

Variant	rs17649801
Chromosome Location	chr15:52255630-52255631
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52251464..52253860-chr15:52255270..52257201,2	K562	blood:
2	chr15:52250643..52258110-chr15:52261122..52265819,12	MCF-7	breast:
3	chr15:52247928..52250434-chr15:52253574..52257568,3	MCF-7	breast:
4	chr15:52249529..52256191-chr15:52262317..52265170,10	MCF-7	breast:
5	chr15:52250021..52252100-chr15:52255558..52257504,2	MCF-7	breast:
6	chr15:52253083..52256570-chr15:52257033..52260699,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166477	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1025185	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10519323	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10519325	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10519326	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12438469	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1426085	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1426086	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17649047	1.00[EUR][1000 genomes]
rs17649178	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17649255	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17649391	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17649692	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17649820	0.91[AMR][1000 genomes]
rs17649826	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17705530	1.00[EUR][1000 genomes]
rs17705649	1.00[EUR][1000 genomes]
rs17705685	1.00[EUR][1000 genomes]
rs17705889	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17706076	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2052707	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162224	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2263946	0.85[ASN][1000 genomes]
rs2436664	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2470609	0.90[ASN][1000 genomes]
rs2470613	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554309	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554310	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554311	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554317	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2554318	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554321	0.90[ASN][1000 genomes]
rs2554323	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554325	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2554326	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2554330	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2554333	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554341	0.88[ASN][1000 genomes]
rs2554351	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554352	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554356	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2570218	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570219	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570220	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570221	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570225	0.92[ASN][1000 genomes]
rs2570227	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570234	0.90[ASN][1000 genomes]
rs2570242	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570244	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2570245	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570246	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2570247	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2570249	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2570250	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2570256	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570257	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570259	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570261	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570262	0.83[ASN][1000 genomes]
rs2570267	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570270	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570273	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2570274	1.00[EUR][1000 genomes]
rs2593165	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2593175	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2593176	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2593180	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623246	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2623248	0.92[ASN][1000 genomes]
rs2623250	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623252	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623253	0.90[ASN][1000 genomes]
rs2623257	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623260	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623264	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623267	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2623268	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623269	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2623277	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623278	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623287	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623293	0.90[ASN][1000 genomes]
rs2899483	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2916174	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2959297	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2959303	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099570	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34407523	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3794533	1.00[EUR][1000 genomes]
rs3794537	1.00[EUR][1000 genomes]
rs4774601	1.00[EUR][1000 genomes]
rs4775979	1.00[EUR][1000 genomes]
rs4775987	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775988	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775989	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775990	0.85[AMR][1000 genomes]
rs7166322	1.00[EUR][1000 genomes]
rs7170429	1.00[EUR][1000 genomes]
rs7170700	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7179139	1.00[EUR][1000 genomes]
rs73411105	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74013606	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8024441	1.00[EUR][1000 genomes]
rs8026507	1.00[EUR][1000 genomes]
rs8027426	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8042310	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919056	0.90[ASN][1000 genomes]
rs919057	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs990666	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1053788	chr15:52223389-52307138	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52179600-52259800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:52200400-52262200	Weak transcription	Stomach Mucosa	stomach
3	chr15:52222600-52259800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:52226200-52259400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:52227400-52258400	Strong transcription	Dnd41	blood
6	chr15:52232800-52256000	Strong transcription	Fetal Muscle Leg	muscle
7	chr15:52233000-52258000	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr15:52233600-52258000	Strong transcription	Primary B cells from peripheral blood	blood
9	chr15:52235600-52256000	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:52235600-52258000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:52235800-52256000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:52235800-52258000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:52235800-52258600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr15:52235800-52259200	Strong transcription	Hela-S3	cervix
15	chr15:52236000-52256200	Strong transcription	HepG2	liver
16	chr15:52236000-52258000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:52236000-52258600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:52236000-52258800	Strong transcription	Fetal Thymus	thymus
19	chr15:52236200-52258800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:52237000-52256000	Strong transcription	Fetal Stomach	stomach
21	chr15:52237000-52258400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr15:52237200-52257600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr15:52244400-52257400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr15:52244600-52262600	Weak transcription	Fetal Heart	heart
25	chr15:52245200-52255800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr15:52245600-52261800	Weak transcription	Pancreas	Pancrea
27	chr15:52245600-52262600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr15:52245800-52258000	Weak transcription	Aorta	Aorta
29	chr15:52245800-52263000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:52245800-52263200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:52246000-52257800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr15:52246400-52262200	Weak transcription	NHLF	lung
33	chr15:52247000-52262400	Weak transcription	Colonic Mucosa	Colon
34	chr15:52249800-52263000	Weak transcription	Psoas Muscle	Psoas
35	chr15:52250200-52256000	Strong transcription	Primary T cells from cord blood	blood
36	chr15:52250400-52258000	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr15:52250600-52258000	Strong transcription	Primary hematopoietic stem cells	blood
38	chr15:52251600-52256000	Strong transcription	NHDF-Ad	bronchial
39	chr15:52252200-52258800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:52252800-52257800	Weak transcription	HUVEC	blood vessel
41	chr15:52253000-52256000	Strong transcription	Fetal Intestine Small	intestine
42	chr15:52253200-52256800	Weak transcription	Primary B cells from cord blood	blood
43	chr15:52253200-52257200	Weak transcription	NH-A	brain
44	chr15:52253200-52257600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr15:52253200-52259600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr15:52253200-52259800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr15:52253200-52262400	Weak transcription	Fetal Brain Male	brain
48	chr15:52253200-52262800	Weak transcription	HSMMtube	muscle
49	chr15:52253200-52263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr15:52253400-52259600	Weak transcription	Brain Angular Gyrus	brain

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