Variant report

Variant	rs17121678
Chromosome Location	chr12:59286349-59286350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59280741..59283382-chr12:59285859..59287924,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139263	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10506358	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11172795	1.00[JPT][hapmap]
rs11172797	1.00[JPT][hapmap]
rs11172799	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12303283	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs17121676	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17121715	1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17617428	1.00[JPT][hapmap]
rs59360671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7957573	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59262600-59295000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:59266000-59311000	Weak transcription	Fetal Thymus	thymus
3	chr12:59273600-59287000	Weak transcription	Stomach Mucosa	stomach
4	chr12:59273800-59289000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:59274800-59289000	Weak transcription	Right Ventricle	heart
6	chr12:59275000-59300800	Weak transcription	HSMMtube	muscle
7	chr12:59275200-59297800	Weak transcription	Hela-S3	cervix
8	chr12:59277800-59288800	Weak transcription	Right Atrium	heart
9	chr12:59279000-59286800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:59279000-59310800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr12:59279200-59290200	Weak transcription	Fetal Heart	heart
12	chr12:59279200-59309400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:59280200-59287400	Weak transcription	Psoas Muscle	Psoas
14	chr12:59281000-59289400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr12:59281200-59287400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:59282400-59286400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:59282400-59286800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:59282400-59287000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:59282400-59290200	Weak transcription	Fetal Brain Female	brain
20	chr12:59282400-59290600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:59282400-59297800	Weak transcription	A549	lung
22	chr12:59282800-59287600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:59282800-59287800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:59283400-59298000	Weak transcription	Fetal Brain Male	brain
25	chr12:59283800-59286800	Weak transcription	Brain Germinal Matrix	brain
26	chr12:59283800-59287200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:59283800-59288800	Weak transcription	Spleen	Spleen
28	chr12:59283800-59300400	Weak transcription	Placenta	Placenta
29	chr12:59284000-59286400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:59284000-59286400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:59284000-59286600	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:59284000-59286600	Strong transcription	HMEC	breast
33	chr12:59284000-59286800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:59284000-59286800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:59284000-59286800	Weak transcription	Small Intestine	intestine
36	chr12:59284000-59287200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:59284000-59287200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:59284000-59287200	Weak transcription	Esophagus	oesophagus
39	chr12:59284000-59287200	Weak transcription	Fetal Kidney	kidney
40	chr12:59284000-59287200	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:59284000-59287200	Weak transcription	Fetal Stomach	stomach
42	chr12:59284000-59287200	Weak transcription	Pancreas	Pancrea
43	chr12:59284000-59287200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:59284000-59287200	Weak transcription	NHLF	lung
45	chr12:59284000-59287400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:59284000-59287400	Weak transcription	Fetal Intestine Small	intestine
47	chr12:59284000-59287400	Weak transcription	Lung	lung
48	chr12:59284000-59287400	Weak transcription	Ovary	ovary
49	chr12:59284000-59287400	Weak transcription	NH-A	brain
50	chr12:59284000-59287600	Weak transcription	Gastric	stomach

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