Variant report

Variant	rs2554331
Chromosome Location	chr15:52157835-52157836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52157498..52159871-chr15:52162459..52164030,2	K562	blood:
2	chr15:52120688..52125353-chr15:52156993..52161402,10	MCF-7	breast:
3	chr15:52152690..52156184-chr15:52157432..52160441,3	K562	blood:
4	chr15:52151375..52154020-chr15:52156501..52159080,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction
ENSG00000259632	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1824083	0.92[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2162224	0.92[YRI][hapmap]
rs2436663	0.87[YRI][hapmap]
rs2436664	0.87[YRI][hapmap]
rs2554319	0.87[YRI][hapmap]
rs2554321	0.81[YRI][hapmap]
rs2554324	0.87[YRI][hapmap]
rs2554329	0.91[YRI][hapmap]
rs2554333	0.87[YRI][hapmap]
rs2554341	0.81[YRI][hapmap]
rs2554346	0.80[YRI][hapmap]
rs2554352	0.87[YRI][hapmap]
rs2554356	0.87[YRI][hapmap]
rs2554357	0.80[YRI][hapmap]
rs2570218	0.86[YRI][hapmap]
rs2570232	0.86[YRI][hapmap]
rs2570242	0.86[YRI][hapmap]
rs2570244	0.87[YRI][hapmap]
rs2570245	0.87[YRI][hapmap]
rs2570246	0.87[YRI][hapmap]
rs2570249	0.86[YRI][hapmap]
rs2570250	0.86[YRI][hapmap]
rs2570256	0.87[YRI][hapmap]
rs2570257	0.87[YRI][hapmap]
rs2570267	0.87[YRI][hapmap]
rs2570270	0.80[YRI][hapmap]
rs2570272	0.80[YRI][hapmap]
rs2570273	0.86[YRI][hapmap]
rs2593171	0.87[YRI][hapmap]
rs2593175	0.87[YRI][hapmap]
rs2593186	0.80[YRI][hapmap]
rs2623246	0.87[YRI][hapmap]
rs2623248	0.87[YRI][hapmap]
rs2623250	0.86[YRI][hapmap]
rs2623264	0.86[YRI][hapmap]
rs2623269	0.87[YRI][hapmap]
rs2623274	0.87[YRI][hapmap]
rs2623277	0.87[YRI][hapmap]
rs2623287	0.86[YRI][hapmap]
rs2623290	0.92[YRI][hapmap]
rs2623293	0.82[YRI][hapmap]
rs2652596	0.92[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs543024	0.92[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs562858	0.92[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs689842	0.93[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs690433	0.93[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7179045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs919057	0.81[YRI][hapmap]
rs990666	0.81[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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52141600-52166800	Weak transcription	Stomach Mucosa	stomach
2	chr15:52141800-52176200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:52145800-52176600	Weak transcription	Psoas Muscle	Psoas
4	chr15:52148200-52176200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:52149000-52161000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:52149400-52171000	Weak transcription	Brain Angular Gyrus	brain
7	chr15:52149800-52160600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:52149800-52168000	Weak transcription	Right Ventricle	heart
9	chr15:52150600-52160800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:52152400-52170000	Weak transcription	Pancreas	Pancrea
11	chr15:52152400-52170800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:52153200-52158400	Genic enhancers	A549	lung
13	chr15:52153200-52161200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:52153200-52161600	Genic enhancers	NHEK	skin
15	chr15:52153400-52158400	Strong transcription	Hela-S3	cervix
16	chr15:52153400-52161600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:52153800-52158000	Strong transcription	GM12878-XiMat	blood
18	chr15:52153800-52178000	Weak transcription	Brain Germinal Matrix	brain
19	chr15:52154000-52161600	Genic enhancers	HMEC	breast
20	chr15:52154400-52159400	Weak transcription	Fetal Heart	heart
21	chr15:52154400-52162000	Weak transcription	Small Intestine	intestine
22	chr15:52154400-52165800	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:52154400-52170200	Weak transcription	Fetal Brain Male	brain
24	chr15:52154800-52158000	Strong transcription	NHLF	lung
25	chr15:52155000-52158000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:52155000-52158000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:52155000-52158000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr15:52155000-52158000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:52155000-52158000	Strong transcription	Adipose Nuclei	Adipose
30	chr15:52155000-52158000	Strong transcription	HSMM	muscle
31	chr15:52155000-52158000	Strong transcription	HUVEC	blood vessel
32	chr15:52155000-52158800	Strong transcription	Fetal Intestine Large	intestine
33	chr15:52155000-52160000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:52155000-52160400	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr15:52155000-52160800	Strong transcription	Duodenum Mucosa	Duodenum
36	chr15:52155000-52162600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:52155000-52162800	Strong transcription	Fetal Stomach	stomach
38	chr15:52155000-52164000	Strong transcription	Primary B cells from cord blood	blood
39	chr15:52155000-52165400	Strong transcription	Dnd41	blood
40	chr15:52155000-52167600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:52155000-52167800	Strong transcription	Primary B cells from peripheral blood	blood
42	chr15:52155000-52169800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr15:52155000-52170800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:52155000-52173600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr15:52155200-52158000	Strong transcription	Left Ventricle	heart
46	chr15:52155200-52158000	Strong transcription	Lung	lung
47	chr15:52155200-52158200	Strong transcription	Fetal Thymus	thymus
48	chr15:52155200-52160400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr15:52155200-52167800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr15:52155200-52169600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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