Variant report

Variant	rs2593171
Chromosome Location	chr15:52218430-52218431
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:52215772-52218495	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52217453..52219965-chr15:52222448..52224988,2	MCF-7	breast:
2	chr15:52209946..52211587-chr15:52217448..52218968,2	MCF-7	breast:

Variant related genes	Relation type
TMOD3	TF binding region
ENSG00000138594	Chromatin interaction
ENSG00000259556	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs11446467	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1426085	0.87[AFR][1000 genomes]
rs1824083	0.80[YRI][hapmap]
rs1867985	0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2162224	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2263946	0.81[AFR][1000 genomes]
rs2436663	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2436664	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2470592	0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470606	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470609	0.83[AFR][1000 genomes]
rs2470614	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554309	0.82[YRI][hapmap]
rs2554310	0.88[YRI][hapmap]
rs2554311	0.87[AFR][1000 genomes]
rs2554312	1.00[AFR][1000 genomes]
rs2554319	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554321	0.93[YRI][hapmap]
rs2554323	0.87[AFR][1000 genomes]
rs2554324	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2554325	0.81[AFR][1000 genomes]
rs2554329	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2554331	0.87[YRI][hapmap]
rs2554333	1.00[YRI][hapmap]
rs2554341	0.93[YRI][hapmap]
rs2554344	0.93[AFR][1000 genomes]
rs2554346	0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554351	0.81[AFR][1000 genomes]
rs2554352	1.00[YRI][hapmap]
rs2554356	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2554357	0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs2570218	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2570220	0.87[AFR][1000 genomes]
rs2570221	0.87[AFR][1000 genomes]
rs2570222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2570223	1.00[AFR][1000 genomes]
rs2570227	0.84[AFR][1000 genomes]
rs2570232	1.00[YRI][hapmap]
rs2570242	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2570244	1.00[YRI][hapmap]
rs2570245	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2570246	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2570247	0.81[AFR][1000 genomes]
rs2570249	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2570250	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2570256	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2570257	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2570261	0.81[AFR][1000 genomes]
rs2570266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2570267	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2570270	0.94[YRI][hapmap];0.80[AFR][1000 genomes]
rs2570272	0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2570273	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2570274	0.85[AFR][1000 genomes]
rs2593165	0.87[AFR][1000 genomes]
rs2593172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593175	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2593176	0.87[AFR][1000 genomes]
rs2593178	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593180	0.87[AFR][1000 genomes]
rs2593186	0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593197	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593203	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2623246	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2623248	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2623250	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2623252	0.81[AFR][1000 genomes]
rs2623264	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2623267	0.81[AFR][1000 genomes]
rs2623269	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2623273	0.93[AFR][1000 genomes]
rs2623274	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2623275	0.93[AFR][1000 genomes]
rs2623277	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2623278	0.87[AFR][1000 genomes]
rs2623287	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2623290	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2623293	0.94[YRI][hapmap]
rs2916174	0.87[AFR][1000 genomes]
rs562858	0.80[YRI][hapmap]
rs689842	0.81[YRI][hapmap]
rs690433	0.81[YRI][hapmap]
rs73396698	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411105	0.81[AFR][1000 genomes]
rs919056	0.87[YRI][hapmap];0.84[AFR][1000 genomes]
rs919057	0.93[YRI][hapmap]
rs919058	0.93[AFR][1000 genomes]
rs990666	0.93[YRI][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	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

No data

Chromatin state (count:122 , 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	chr15:52179800-52218600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:52181200-52221000	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr15:52183200-52223000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:52186400-52219000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:52191000-52222800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:52193400-52227800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:52193400-52232800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:52193600-52233600	Weak transcription	Fetal Brain Male	brain
10	chr15:52194200-52228200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr15:52194200-52231600	Weak transcription	Psoas Muscle	Psoas
12	chr15:52194400-52236800	Weak transcription	Fetal Kidney	kidney
13	chr15:52194400-52239000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:52196200-52234000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:52197000-52234200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:52197000-52234800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:52198400-52219000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:52200400-52220800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:52200400-52262200	Weak transcription	Stomach Mucosa	stomach
20	chr15:52201000-52238800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr15:52201800-52223000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr15:52202000-52230000	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr15:52204600-52224600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:52204800-52218800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:52204800-52219400	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr15:52204800-52238800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:52207400-52219600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:52208000-52219000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr15:52208000-52222800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:52208200-52218600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:52208200-52219200	Strong transcription	Fetal Lung	lung
32	chr15:52208400-52218600	Strong transcription	Primary T cells from cord blood	blood
33	chr15:52209000-52218600	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr15:52209400-52219400	Strong transcription	NHEK	skin
35	chr15:52210000-52233600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr15:52210000-52239000	Weak transcription	Colon Smooth Muscle	Colon
37	chr15:52210200-52224200	Strong transcription	A549	lung
38	chr15:52210400-52218600	Strong transcription	GM12878-XiMat	blood
39	chr15:52211200-52230400	Weak transcription	K562	blood
40	chr15:52211600-52228800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:52211600-52237600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr15:52211600-52239200	Weak transcription	Right Ventricle	heart
43	chr15:52212200-52219400	Strong transcription	Liver	Liver
44	chr15:52212400-52241600	Weak transcription	Small Intestine	intestine
45	chr15:52212800-52221000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:52213000-52218600	Strong transcription	Thymus	Thymus
47	chr15:52213000-52223400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:52214000-52226200	Weak transcription	Ovary	ovary
49	chr15:52215200-52219000	Weak transcription	HSMM	muscle
50	chr15:52215200-52223000	Weak transcription	NHDF-Ad	bronchial

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