Variant report

Variant	rs2623258
Chromosome Location	chr15:52101594-52101595
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52100222..52103696-chr15:52103888..52107125,3	MCF-7	breast:
2	chr15:52099817..52103659-chr15:52120631..52123209,5	MCF-7	breast:
3	chr15:52100848..52103641-chr15:52104210..52107534,4	K562	blood:
4	chr15:52100912..52103641-chr15:52104317..52106256,2	K562	blood:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1133878	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964482	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16964483	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17611465	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1863429	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1972419	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991267	1.00[CHB][hapmap]
rs2016057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124587	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2258248	1.00[CHB][hapmap]
rs2448810	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2554354	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554355	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554358	0.96[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570243	0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593169	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2593181	1.00[CHB][hapmap]
rs2606128	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2606130	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606133	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606147	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622765	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2623245	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623247	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623251	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623263	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623270	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652597	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28522862	1.00[ASN][1000 genomes]
rs28654101	1.00[ASN][1000 genomes]
rs28876142	1.00[ASN][1000 genomes]
rs2959296	1.00[CHB][hapmap]
rs691738	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71472920	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	esv3361968	chr15:52087428-52107237	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2623258	RP11-707P17.1	cis	Nerve Tibial	GTEx
rs2623258	SCG3	cis	Cerebellum	GTEx
rs2623258	SCG3	cis	Temporal Cortex	GTEx
rs2623258	SCG3	cis	Brain Pons	GTEx
rs2623258	SCG3	cis	Frontal Cortex	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52052200-52101800	Weak transcription	Colonic Mucosa	Colon
2	chr15:52052600-52106600	Weak transcription	HSMM	muscle
3	chr15:52060200-52103400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:52060800-52102600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:52060800-52105400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:52061600-52112000	Weak transcription	NHLF	lung
7	chr15:52074800-52102800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr15:52076800-52104400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr15:52080800-52102600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:52085800-52105200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr15:52085800-52108800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:52089000-52106400	Weak transcription	HSMMtube	muscle
13	chr15:52089200-52107200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr15:52090400-52104400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr15:52091200-52104600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:52091200-52109400	Weak transcription	Gastric	stomach
17	chr15:52091400-52103600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr15:52091800-52108200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:52092000-52107800	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:52093400-52101800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:52093600-52105200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr15:52093800-52108600	Weak transcription	Fetal Lung	lung
23	chr15:52095000-52101800	Weak transcription	Psoas Muscle	Psoas
24	chr15:52095800-52101800	Strong transcription	Brain Hippocampus Middle	brain
25	chr15:52096000-52104800	Weak transcription	Placenta	Placenta
26	chr15:52097200-52103000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr15:52097600-52102000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr15:52098200-52102000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:52098400-52101600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:52098400-52101800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:52098400-52102000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:52098400-52102000	Strong transcription	Brain Angular Gyrus	brain
33	chr15:52098400-52104000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:52098400-52104400	Strong transcription	Brain Anterior Caudate	brain
35	chr15:52098400-52104400	Strong transcription	Brain Cingulate Gyrus	brain
36	chr15:52098400-52106800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:52098600-52102400	Strong transcription	Adipose Nuclei	Adipose
38	chr15:52098800-52108800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:52099000-52103000	Strong transcription	Colon Smooth Muscle	Colon
40	chr15:52099200-52107400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr15:52099200-52108800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:52099400-52102200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:52099400-52107200	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr15:52099600-52108600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr15:52099600-52108800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr15:52099800-52101600	Weak transcription	Brain Substantia Nigra	brain
47	chr15:52099800-52103600	Weak transcription	Ovary	ovary
48	chr15:52099800-52108400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr15:52099800-52109000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr15:52099800-52109400	Weak transcription	Spleen	Spleen

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