Variant report

Variant	rs2623248
Chromosome Location	chr15:52140159-52140160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52137753..52140319-chr15:52187826..52190548,2	MCF-7	breast:
2	chr15:52121713..52124493-chr15:52139618..52143592,4	MCF-7	breast:
3	chr15:52132428..52137559-chr15:52138263..52141048,4	MCF-7	breast:
4	chr15:52139835..52141814-chr15:52148000..52150770,2	MCF-7	breast:
5	chr15:52139382..52141080-chr15:52142666..52144648,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1025185	0.87[ASN][1000 genomes]
rs10519325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10519326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12438469	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1426085	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1426086	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16964523	0.86[JPT][hapmap]
rs17649047	0.86[JPT][hapmap]
rs17649255	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17649391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17649692	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17649801	0.92[ASN][1000 genomes]
rs17705889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17706076	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1867985	0.94[YRI][hapmap]
rs2052707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2162224	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2263946	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2436663	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2436664	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2470592	0.93[YRI][hapmap]
rs2470609	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2470613	0.92[ASN][1000 genomes]
rs2554309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2554310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2554311	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2554312	0.81[AFR][1000 genomes]
rs2554317	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2554318	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2554319	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2554320	0.81[AFR][1000 genomes]
rs2554321	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]
rs2554323	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2554324	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2554325	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2554326	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2554329	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2554330	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2554331	0.87[YRI][hapmap]
rs2554333	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2554341	0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2554344	0.87[AFR][1000 genomes]
rs2554346	0.94[YRI][hapmap]
rs2554351	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2554352	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2554356	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2554357	0.94[YRI][hapmap]
rs2570218	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570219	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570220	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570221	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570222	0.81[AFR][1000 genomes]
rs2570223	0.81[AFR][1000 genomes]
rs2570225	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570227	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570232	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2570234	0.97[ASN][1000 genomes]
rs2570242	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570244	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2570245	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570246	0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2570247	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2570249	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2570250	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2570256	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570257	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570259	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570261	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570262	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2570266	0.81[AFR][1000 genomes]
rs2570267	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2570270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2570272	0.94[YRI][hapmap]
rs2570273	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2570274	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2593165	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2593171	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2593172	0.81[AFR][1000 genomes]
rs2593175	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2593176	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2593180	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2593186	0.94[YRI][hapmap]
rs2623246	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2623250	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623252	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623253	0.97[ASN][1000 genomes]
rs2623257	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2623260	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623261	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2623264	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623267	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2623268	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623269	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2623273	0.87[AFR][1000 genomes]
rs2623274	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2623275	0.87[AFR][1000 genomes]
rs2623277	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623278	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623287	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623290	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2623293	0.85[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2899483	0.84[ASN][1000 genomes]
rs2916174	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2959297	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2959303	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3099570	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs34407523	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4775987	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4775988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4775989	0.92[ASN][1000 genomes]
rs689842	0.81[YRI][hapmap]
rs690433	0.81[YRI][hapmap]
rs7166322	0.86[JPT][hapmap]
rs7170700	0.81[ASN][1000 genomes]
rs73411105	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74013606	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8027426	0.86[JPT][hapmap]
rs8042310	0.92[ASN][1000 genomes]
rs919056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs919057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs919058	0.87[AFR][1000 genomes]
rs990666	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]

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:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52129000-52140200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:52130000-52155000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr15:52130800-52155200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr15:52132200-52140200	Enhancers	Primary T cells from cord blood	blood
5	chr15:52133000-52143600	Enhancers	NHDF-Ad	bronchial
6	chr15:52133000-52146200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:52134600-52142000	Enhancers	NHLF	lung
8	chr15:52135600-52140200	Weak transcription	Ovary	ovary
9	chr15:52135800-52146200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr15:52135800-52155000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr15:52136000-52145800	Weak transcription	Liver	Liver
12	chr15:52136000-52155200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:52136200-52155000	Weak transcription	Aorta	Aorta
14	chr15:52136600-52153400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr15:52137200-52140600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr15:52137200-52141600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr15:52137400-52147400	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:52137600-52141000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr15:52137600-52141400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr15:52137600-52145600	Weak transcription	HepG2	liver
21	chr15:52137800-52140400	Enhancers	Thymus	Thymus
22	chr15:52137800-52155000	Weak transcription	Fetal Intestine Large	intestine
23	chr15:52138000-52141200	Weak transcription	Pancreas	Pancrea
24	chr15:52138000-52153400	Weak transcription	Esophagus	oesophagus
25	chr15:52138000-52155000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:52138600-52155000	Weak transcription	Fetal Muscle Leg	muscle
27	chr15:52139000-52141800	Enhancers	HUVEC	blood vessel
28	chr15:52139000-52146000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:52139000-52153400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:52139200-52140400	Enhancers	HSMM	muscle
31	chr15:52139200-52141000	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:52139200-52141000	Weak transcription	Fetal Stomach	stomach
33	chr15:52139200-52141000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr15:52139200-52141000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:52139200-52141200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr15:52139200-52147600	Weak transcription	Brain Anterior Caudate	brain
37	chr15:52139200-52156200	Weak transcription	Fetal Intestine Small	intestine
38	chr15:52139400-52140200	Weak transcription	Stomach Mucosa	stomach
39	chr15:52139400-52140200	Enhancers	HSMMtube	muscle
40	chr15:52139400-52140800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:52139400-52141000	Weak transcription	Right Atrium	heart
42	chr15:52139400-52141200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:52139400-52141200	Weak transcription	Left Ventricle	heart
44	chr15:52139400-52141200	Weak transcription	Psoas Muscle	Psoas
45	chr15:52139400-52141800	Weak transcription	Right Ventricle	heart
46	chr15:52139400-52142400	Weak transcription	Spleen	Spleen
47	chr15:52139400-52142600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:52139400-52142800	Weak transcription	K562	blood
49	chr15:52139400-52143000	Weak transcription	Lung	lung
50	chr15:52139400-52144800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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