Variant report

Variant	rs2554321
Chromosome Location	chr15:52234532-52234533
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52232725..52234796-chr15:52242027..52243795,2	MCF-7	breast:
2	chr15:52230761..52232495-chr15:52232835..52234665,3	MCF-7	breast:
3	chr15:52232743..52235085-chr15:52238669..52241010,2	MCF-7	breast:

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1025185	0.86[ASN][1000 genomes]
rs10519325	0.82[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs10519326	0.82[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs12438469	0.83[ASN][1000 genomes]
rs1426085	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1426086	0.82[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs16964523	0.82[MEX][hapmap];1.00[TSI][hapmap]
rs16964657	1.00[EUR][1000 genomes]
rs16964694	0.80[MEX][hapmap]
rs16964720	1.00[GIH][hapmap]
rs17649047	0.90[MEX][hapmap];1.00[TSI][hapmap]
rs17649255	0.88[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs17649391	0.82[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs17649692	0.82[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17649801	0.90[ASN][1000 genomes]
rs17705889	0.82[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs17706076	0.82[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs1867985	0.87[YRI][hapmap]
rs2052707	0.82[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2162224	0.82[CHB][hapmap];0.84[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2246726	1.00[GIH][hapmap];0.91[MEX][hapmap]
rs2250797	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2263946	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2433219	1.00[EUR][1000 genomes]
rs2436663	0.93[YRI][hapmap]
rs2436664	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2470592	0.86[ASW][hapmap];0.93[MKK][hapmap];0.87[YRI][hapmap]
rs2470609	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2470613	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2554309	0.82[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2554310	0.82[CHB][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2554311	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2554317	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554318	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2554319	0.93[YRI][hapmap]
rs2554323	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2554324	0.93[YRI][hapmap]
rs2554325	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2554326	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2554329	0.91[YRI][hapmap]
rs2554330	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2554331	0.81[YRI][hapmap]
rs2554333	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2554338	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2554341	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2554346	0.87[YRI][hapmap]
rs2554351	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2554352	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2554356	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2554357	0.87[YRI][hapmap]
rs2570218	0.86[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2570219	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2570220	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2570221	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2570225	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2570227	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2570232	0.87[ASW][hapmap];0.91[MEX][hapmap];0.93[YRI][hapmap]
rs2570234	0.81[ASN][1000 genomes]
rs2570242	0.86[ASW][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2570244	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2570245	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2570246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2570247	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2570249	0.86[ASW][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2570250	0.86[ASW][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2570256	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2570257	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2570259	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2570261	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2570262	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2570267	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2570270	0.82[CHB][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2570272	0.87[YRI][hapmap]
rs2570273	0.86[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2570274	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2593165	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2593171	0.93[YRI][hapmap]
rs2593175	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2593176	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2593180	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2593186	0.93[YRI][hapmap]
rs2593189	1.00[GIH][hapmap]
rs2593196	0.80[AMR][1000 genomes]
rs2623246	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2623248	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2623250	0.86[ASW][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2623252	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2623253	0.81[ASN][1000 genomes]
rs2623257	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2623260	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2623261	0.80[AMR][1000 genomes]
rs2623264	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2623267	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2623268	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2623269	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2623274	0.93[YRI][hapmap]
rs2623277	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2623278	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2623287	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2623290	0.92[YRI][hapmap]
rs2623293	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2916174	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2959297	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2959303	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3099570	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs34407523	0.83[ASN][1000 genomes]
rs4775971	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs4775987	0.83[ASN][1000 genomes]
rs4775988	0.82[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4775989	0.90[ASN][1000 genomes]
rs4775995	1.00[GIH][hapmap]
rs4775996	1.00[GIH][hapmap]
rs4775997	1.00[GIH][hapmap]
rs59782457	1.00[EUR][1000 genomes]
rs7166322	0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7173661	0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7177328	1.00[GIH][hapmap]
rs73411105	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs74013606	0.81[ASN][1000 genomes]
rs8027426	0.90[MEX][hapmap];1.00[TSI][hapmap]
rs8042310	0.90[ASN][1000 genomes]
rs919056	0.82[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs919057	0.82[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs990666	0.82[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.83[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:124 , 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	chr15:52194400-52236800	Weak transcription	Fetal Kidney	kidney
3	chr15:52194400-52239000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:52197000-52234800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:52200400-52262200	Weak transcription	Stomach Mucosa	stomach
6	chr15:52201000-52238800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:52204800-52238800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:52210000-52239000	Weak transcription	Colon Smooth Muscle	Colon
9	chr15:52211600-52237600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr15:52211600-52239200	Weak transcription	Right Ventricle	heart
11	chr15:52212400-52241600	Weak transcription	Small Intestine	intestine
12	chr15:52216000-52238600	Weak transcription	Pancreas	Pancrea
13	chr15:52217200-52238400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:52217200-52238800	Weak transcription	Brain Angular Gyrus	brain
15	chr15:52217600-52238800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:52217800-52237400	Weak transcription	Aorta	Aorta
17	chr15:52217800-52237400	Weak transcription	Brain Anterior Caudate	brain
18	chr15:52217800-52239000	Weak transcription	Gastric	stomach
19	chr15:52218000-52243200	Weak transcription	Fetal Heart	heart
20	chr15:52222600-52259800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:52222800-52236200	Strong transcription	Fetal Stomach	stomach
22	chr15:52223200-52245400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:52224000-52237400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:52224200-52237200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:52226000-52255200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:52226200-52234600	Strong transcription	Fetal Thymus	thymus
27	chr15:52226200-52242600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:52226200-52254800	Strong transcription	Thymus	Thymus
29	chr15:52226200-52255000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr15:52226200-52259400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:52226800-52237200	Weak transcription	Spleen	Spleen
32	chr15:52227000-52235600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:52227400-52234800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr15:52227400-52255000	Strong transcription	Liver	Liver
35	chr15:52227400-52258400	Strong transcription	Dnd41	blood
36	chr15:52227600-52235000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr15:52227800-52234800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr15:52227800-52234800	Strong transcription	Fetal Intestine Large	intestine
39	chr15:52227800-52255000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr15:52228200-52234600	Strong transcription	HepG2	liver
41	chr15:52228200-52235200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:52228400-52234800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:52228400-52238400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr15:52228600-52236400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr15:52229200-52237000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr15:52229200-52238200	Weak transcription	Brain Germinal Matrix	brain
47	chr15:52229400-52249000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr15:52229800-52254200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:52230000-52235000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr15:52230000-52237400	Weak transcription	Ovary	ovary

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