Variant report

Variant	rs17012823
Chromosome Location	chr3:23259724-23259725
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23245705..23247404-chr3:23258369..23260756,2	K562	blood:
2	chr3:23247857..23249626-chr3:23258764..23261200,2	MCF-7	breast:
3	chr3:23252644..23254931-chr3:23257139..23259977,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10510537	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs13077333	0.83[ASN][1000 genomes]
rs13083654	0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs13087234	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs13095887	0.86[JPT][hapmap]
rs1495132	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17012834	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17012844	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17012852	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17012861	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17012897	0.84[ASN][1000 genomes]
rs17012927	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs17012943	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes]
rs17012959	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs17012969	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs17012988	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs17012998	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs17013003	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs17013023	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs17013026	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs17013029	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs17013035	1.00[CEU][hapmap];0.80[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs17013049	0.91[AMR][1000 genomes]
rs17013104	1.00[CEU][hapmap];0.80[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs17013116	1.00[CEU][hapmap];0.80[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17013125	1.00[CEU][hapmap];0.80[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs17013128	1.00[CEU][hapmap];0.80[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs17013152	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2014132	0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2291720	0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34239585	0.87[ASN][1000 genomes]
rs34259979	0.87[ASN][1000 genomes]
rs35024744	0.86[ASN][1000 genomes]
rs35743404	0.87[ASN][1000 genomes]
rs36004369	0.83[ASN][1000 genomes]
rs58844120	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59365170	0.91[AMR][1000 genomes]
rs60709653	0.91[AMR][1000 genomes]
rs73044305	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs73044309	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs73044318	0.91[AMR][1000 genomes]
rs73044329	0.91[AMR][1000 genomes]
rs73044337	0.91[AMR][1000 genomes]
rs73044339	0.91[AMR][1000 genomes]
rs73050236	0.91[AMR][1000 genomes]
rs73050238	0.91[AMR][1000 genomes]
rs73050257	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs73050270	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs73050276	0.96[AMR][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	nsv834636	chr3:23138653-23301443	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23245800-23262800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:23246000-23260800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:23246200-23260600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:23246200-23264200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:23246400-23261200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr3:23246400-23273400	Weak transcription	Aorta	Aorta
7	chr3:23246600-23260000	Weak transcription	NHEK	skin
8	chr3:23246600-23260800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:23246600-23262400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:23246800-23259800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:23248200-23260600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:23248800-23265800	Weak transcription	Primary T cells from cord blood	blood
13	chr3:23249000-23273400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:23249400-23260600	Weak transcription	HSMMtube	muscle
15	chr3:23251600-23260400	Weak transcription	HMEC	breast
16	chr3:23251600-23262800	Weak transcription	Adipose Nuclei	Adipose
17	chr3:23251800-23260600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:23251800-23260600	Weak transcription	Esophagus	oesophagus
19	chr3:23251800-23260800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:23252800-23260600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:23253400-23260800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:23255600-23260600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:23257000-23263200	Enhancers	Brain Hippocampus Middle	brain
24	chr3:23257600-23260600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:23258200-23259800	Enhancers	Fetal Heart	heart
26	chr3:23258400-23260000	Strong transcription	Primary B cells from cord blood	blood
27	chr3:23258600-23260600	Weak transcription	Right Ventricle	heart
28	chr3:23258800-23259800	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr3:23259000-23260600	Weak transcription	Ovary	ovary
30	chr3:23259000-23260600	Weak transcription	Psoas Muscle	Psoas
31	chr3:23259000-23261200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr3:23259000-23261400	Enhancers	A549	lung
33	chr3:23259000-23261400	Enhancers	NHLF	lung
34	chr3:23259000-23262200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr3:23259000-23262600	Enhancers	Colon Smooth Muscle	Colon
36	chr3:23259200-23259800	Enhancers	NH-A	brain
37	chr3:23259200-23260000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:23259200-23260000	Flanking Active TSS	GM12878-XiMat	blood
39	chr3:23259400-23260000	Enhancers	Osteobl	bone
40	chr3:23259400-23261600	Enhancers	HSMM	muscle
41	chr3:23259400-23262400	Enhancers	Liver	Liver
42	chr3:23259600-23260200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:23259600-23260600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:23259600-23260600	Weak transcription	Brain Angular Gyrus	brain
45	chr3:23259600-23260600	Weak transcription	Brain Anterior Caudate	brain
46	chr3:23259600-23260600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:23259600-23260600	Weak transcription	Brain Substantia Nigra	brain
48	chr3:23259600-23260600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:23259600-23260600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:23259600-23260800	Weak transcription	Rectal Smooth Muscle	rectum

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