Variant report

Variant	rs28657676
Chromosome Location	chr15:52637802-52637803
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52629612..52632339-chr15:52635777..52638490,2	K562	blood:
2	chr15:52632217..52635476-chr15:52636789..52639716,4	MCF-7	breast:
3	chr15:52636739..52638418-chr15:52656759..52658437,2	MCF-7	breast:
4	chr15:52586224..52587758-chr15:52636445..52638760,2	MCF-7	breast:
5	chr15:52630806..52632782-chr15:52635293..52638490,3	K562	blood:
6	chr15:52636940..52638490-chr15:52642480..52645431,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197535	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10518683	0.95[AFR][1000 genomes]
rs1108808	1.00[AMR][1000 genomes]
rs12101973	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13329278	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13329402	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13329500	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16964891	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16964910	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16964915	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16964919	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16964921	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16964924	1.00[AMR][1000 genomes]
rs16964928	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2414137	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2414138	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28367336	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28374631	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28409636	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28409760	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28462026	1.00[AMR][1000 genomes]
rs28475475	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28479614	1.00[AMR][1000 genomes]
rs28496242	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28503750	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28508266	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28514341	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28532168	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28556657	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28590330	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28594692	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28618215	1.00[AMR][1000 genomes]
rs28633243	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28650960	1.00[AMR][1000 genomes]
rs28653534	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28669685	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28693941	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28756182	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3764230	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4499185	1.00[AMR][1000 genomes]
rs4624108	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4987194	1.00[AMR][1000 genomes]
rs58029714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58812575	1.00[AMR][1000 genomes]
rs7163242	1.00[AMR][1000 genomes]
rs7164164	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7164872	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7167181	1.00[AMR][1000 genomes]
rs7167680	1.00[AMR][1000 genomes]
rs7167890	0.91[AMR][1000 genomes]
rs7167916	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7168251	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7169104	1.00[AMR][1000 genomes]
rs7169346	1.00[AMR][1000 genomes]
rs7170622	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7182148	1.00[AMR][1000 genomes]
rs73408408	1.00[AMR][1000 genomes]
rs73408415	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408465	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408469	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408478	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73410713	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73410715	1.00[AMR][1000 genomes]
rs744501	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8023623	1.00[AMR][1000 genomes]
rs8024412	0.92[AMR][1000 genomes]
rs8024624	1.00[AMR][1000 genomes]
rs8027637	1.00[AMR][1000 genomes]
rs8027777	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8035199	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8040369	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8040558	0.85[AFR][1000 genomes]
rs8041819	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8042235	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8042245	0.92[AMR][1000 genomes]
rs876549	1.00[AMR][1000 genomes]
rs9744852	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9920739	0.97[AFR][1000 genomes];1.00[AMR][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	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3435837	chr15:52637616-52637812	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52597800-52643400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:52600800-52646600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:52601000-52643400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
5	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:52610000-52643400	Weak transcription	Placenta	Placenta
7	chr15:52611600-52650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:52611800-52675800	Weak transcription	Gastric	stomach
9	chr15:52613000-52642600	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:52613600-52666600	Weak transcription	Right Ventricle	heart
11	chr15:52614800-52642600	Weak transcription	Esophagus	oesophagus
12	chr15:52614800-52653200	Weak transcription	Colonic Mucosa	Colon
13	chr15:52619800-52640600	Weak transcription	Left Ventricle	heart
14	chr15:52619800-52641200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:52620000-52652200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr15:52620600-52659200	Weak transcription	Fetal Lung	lung
17	chr15:52621200-52666600	Weak transcription	Fetal Brain Male	brain
18	chr15:52621800-52640200	Weak transcription	Fetal Brain Female	brain
19	chr15:52621800-52662200	Weak transcription	Psoas Muscle	Psoas
20	chr15:52623800-52644200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:52624200-52641200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:52624600-52641200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:52624600-52641400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:52624600-52642400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr15:52627000-52646600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:52627200-52641200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:52627400-52641400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr15:52629400-52638000	Weak transcription	Brain Substantia Nigra	brain
29	chr15:52629800-52640600	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:52630000-52640600	Weak transcription	Brain Anterior Caudate	brain
31	chr15:52630000-52641400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr15:52630000-52641600	Weak transcription	Primary T cells from cord blood	blood
33	chr15:52630200-52641400	Weak transcription	Brain Angular Gyrus	brain
34	chr15:52630200-52641400	Weak transcription	Osteobl	bone
35	chr15:52630200-52641600	Weak transcription	NHDF-Ad	bronchial
36	chr15:52630600-52641400	Weak transcription	Fetal Thymus	thymus
37	chr15:52630600-52684800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr15:52630800-52640200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:52631000-52638800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr15:52631200-52641400	Weak transcription	HMEC	breast
41	chr15:52631600-52679200	Weak transcription	Fetal Intestine Small	intestine
42	chr15:52632400-52638000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr15:52632600-52640200	Weak transcription	Aorta	Aorta
44	chr15:52632600-52641400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:52632600-52641400	Weak transcription	Fetal Stomach	stomach
46	chr15:52632600-52641400	Weak transcription	Ovary	ovary
47	chr15:52632600-52641400	Weak transcription	Pancreas	Pancrea
48	chr15:52632600-52641400	Weak transcription	Spleen	Spleen
49	chr15:52632600-52641400	Weak transcription	Dnd41	blood
50	chr15:52632600-52643200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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