Variant report

Variant	rs17615589
Chromosome Location	chr2:172930550-172930551
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172928306..172931524-chr2:172948301..172950748,4	MCF-7	breast:
2	chr2:172929662..172931943-chr2:172933111..172935492,3	MCF-7	breast:
3	chr2:172930135..172933791-chr2:172934281..172936934,5	K562	blood:

Variant related genes	Relation type
ENSG00000144355	Chromatin interaction
ENSG00000172878	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10167594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10171214	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10203462	0.91[ASN][1000 genomes]
rs10209911	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1038564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10497377	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11892858	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12052482	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12328877	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12616766	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12622144	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12622385	0.85[AMR][1000 genomes]
rs13403822	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1344393	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17581481	0.85[AMR][1000 genomes]
rs17581509	0.85[AMR][1000 genomes]
rs17581610	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs17615352	0.85[AMR][1000 genomes]
rs17615607	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357323	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796058	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs56923699	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57377675	0.85[AMR][1000 genomes]
rs57656367	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6751078	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs705870	0.82[JPT][hapmap]
rs73976544	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73976547	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs788164	0.90[JPT][hapmap]

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	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv875412	chr2:172903124-172942448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172911200-172947200	Weak transcription	HSMM	muscle
2	chr2:172914000-172937000	Weak transcription	Pancreas	Pancrea
3	chr2:172917400-172934800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:172917800-172932000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr2:172917800-172944800	Weak transcription	Brain Substantia Nigra	brain
6	chr2:172918000-172932800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:172918600-172935600	Weak transcription	Fetal Kidney	kidney
8	chr2:172918600-172935800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:172921800-172937200	Weak transcription	HepG2	liver
10	chr2:172923600-172939800	Weak transcription	Psoas Muscle	Psoas
11	chr2:172924200-172935800	Weak transcription	Adipose Nuclei	Adipose
12	chr2:172924400-172931400	Weak transcription	Primary B cells from cord blood	blood
13	chr2:172925600-172931000	Weak transcription	HSMMtube	muscle
14	chr2:172925600-172932400	Weak transcription	Dnd41	blood
15	chr2:172925800-172937200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:172925800-172937400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:172925800-172942400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:172926000-172931000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:172926000-172932000	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:172926200-172933200	Weak transcription	Aorta	Aorta
21	chr2:172926200-172933400	Weak transcription	Right Ventricle	heart
22	chr2:172926400-172935200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:172926600-172933400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:172927000-172933800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr2:172927200-172931400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:172927200-172931600	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:172927200-172941600	Weak transcription	Gastric	stomach
28	chr2:172927600-172933200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:172927600-172933400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr2:172927800-172931400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:172927800-172936800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:172928200-172935800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:172928400-172932200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:172928400-172932600	Weak transcription	Fetal Heart	heart
35	chr2:172928600-172933600	Weak transcription	Spleen	Spleen
36	chr2:172928600-172937400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:172928600-172940000	Weak transcription	Left Ventricle	heart
38	chr2:172929000-172931000	Weak transcription	K562	blood
39	chr2:172929000-172933000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr2:172929200-172931000	Weak transcription	Ovary	ovary
41	chr2:172929400-172933400	Weak transcription	GM12878-XiMat	blood
42	chr2:172929600-172931000	Enhancers	Brain Germinal Matrix	brain
43	chr2:172930000-172930600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:172930000-172931600	Strong transcription	Primary T cells from cord blood	blood
45	chr2:172930000-172932800	Weak transcription	Brain Anterior Caudate	brain
46	chr2:172930000-172933000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:172930200-172933600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:172930200-172933800	Weak transcription	Fetal Muscle Leg	muscle

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