Variant report

Variant	rs232850
Chromosome Location	chr1:59123531-59123532
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:59037535..59044875-chr1:59111123..59123546,29	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TACSTD2-2	chr1:59120412-59124660	NONHSAT003510

Variant related genes	Relation type
ENSG00000184292	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs232868	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs232883	0.87[AMR][1000 genomes]
rs2746078	0.87[AMR][1000 genomes]
rs2746079	0.87[AMR][1000 genomes]
rs2746080	0.87[AMR][1000 genomes]
rs2811859	0.87[AMR][1000 genomes]
rs2811864	0.87[AMR][1000 genomes]
rs2811871	0.87[AMR][1000 genomes]
rs2811889	0.87[AMR][1000 genomes]
rs2811892	0.87[AMR][1000 genomes]
rs504996	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs522103	1.00[YRI][hapmap];0.87[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS 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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59102000-59130400	Weak transcription	Aorta	Aorta
2	chr1:59108200-59130400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:59110400-59123600	Weak transcription	HSMMtube	muscle
4	chr1:59110800-59125200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:59112800-59125600	Weak transcription	NHLF	lung
6	chr1:59114400-59130200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:59115000-59132800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:59115400-59123800	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:59115600-59124400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:59115600-59138400	Weak transcription	Small Intestine	intestine
11	chr1:59115800-59124800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:59115800-59125000	Weak transcription	Fetal Brain Female	brain
13	chr1:59115800-59129800	Weak transcription	Brain Germinal Matrix	brain
14	chr1:59116000-59129200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:59116000-59129200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:59116000-59151600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:59116400-59123600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr1:59116400-59125200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:59116400-59137800	Weak transcription	Fetal Heart	heart
20	chr1:59116800-59131400	Weak transcription	Fetal Stomach	stomach
21	chr1:59117000-59125200	Weak transcription	Fetal Kidney	kidney
22	chr1:59117800-59147600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:59118000-59139000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:59118200-59127200	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:59118200-59130400	Weak transcription	Brain Anterior Caudate	brain
26	chr1:59118200-59163400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:59118400-59125400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:59118400-59129600	Weak transcription	Fetal Brain Male	brain
29	chr1:59118400-59129600	Weak transcription	Stomach Mucosa	stomach
30	chr1:59118400-59130000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:59118600-59147400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:59118800-59130200	Weak transcription	Brain Angular Gyrus	brain
33	chr1:59118800-59130400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:59119000-59135200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr1:59119200-59130400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:59119800-59147600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:59119800-59155000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:59119800-59162200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:59119800-59163200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:59120000-59143000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:59120000-59153400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:59120200-59149400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:59121000-59123800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:59121000-59161200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:59121200-59130400	Strong transcription	Adipose Nuclei	Adipose
46	chr1:59121200-59141600	Strong transcription	Primary B cells from cord blood	blood
47	chr1:59121400-59124400	Strong transcription	Primary hematopoietic stem cells	blood
48	chr1:59121400-59134800	Strong transcription	Placenta	Placenta
49	chr1:59121400-59145400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:59121400-59161000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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