Variant report

Variant	rs13430424
Chromosome Location	chr2:48423854-48423855
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	chr2:48415132..48417658-chr2:48422363..48423907,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10164456	1.00[AMR][1000 genomes]
rs10165262	1.00[AMR][1000 genomes]
rs10167097	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10168301	1.00[AMR][1000 genomes]
rs10169977	1.00[AMR][1000 genomes]
rs10170181	1.00[AMR][1000 genomes]
rs10171243	1.00[AMR][1000 genomes]
rs10177012	1.00[AMR][1000 genomes]
rs10180159	1.00[AMR][1000 genomes]
rs10180254	1.00[AMR][1000 genomes]
rs10186155	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10187019	1.00[AMR][1000 genomes]
rs10187502	1.00[AMR][1000 genomes]
rs10192404	1.00[AMR][1000 genomes]
rs10198245	1.00[AMR][1000 genomes]
rs10199098	1.00[AMR][1000 genomes]
rs10199615	1.00[AMR][1000 genomes]
rs10200180	1.00[AMR][1000 genomes]
rs10204343	1.00[AMR][1000 genomes]
rs10206551	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10208042	1.00[AMR][1000 genomes]
rs10209432	1.00[AMR][1000 genomes]
rs11683689	0.89[AFR][1000 genomes]
rs13387285	1.00[AMR][1000 genomes]
rs13387357	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13390201	1.00[AMR][1000 genomes]
rs13391880	1.00[AMR][1000 genomes]
rs13396735	1.00[AMR][1000 genomes]
rs13397110	1.00[AMR][1000 genomes]
rs13397541	1.00[AMR][1000 genomes]
rs13408320	1.00[AMR][1000 genomes]
rs13410143	1.00[AMR][1000 genomes]
rs13418349	1.00[AMR][1000 genomes]
rs13419687	1.00[AMR][1000 genomes]
rs13422341	1.00[AMR][1000 genomes]
rs13424841	1.00[AMR][1000 genomes]
rs28623311	1.00[AMR][1000 genomes]
rs28775335	1.00[AMR][1000 genomes]
rs28784960	1.00[AMR][1000 genomes]
rs28893847	1.00[AMR][1000 genomes]
rs7340280	1.00[AMR][1000 genomes]
rs7355330	1.00[AMR][1000 genomes]
rs7355518	1.00[AMR][1000 genomes]
rs9653522	1.00[AMR][1000 genomes]
rs9653523	1.00[AMR][1000 genomes]
rs9653524	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv581773	chr2:48277490-48443109	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1005241	chr2:48413134-48493182	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2762552	chr2:48413146-48493182	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv457407	chr2:48414735-48493182	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv581774	chr2:48414735-48493182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1001850	chr2:48421389-48492090	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv535681	chr2:48421389-48492090	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv3401507	chr2:48423464-48423918	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48421400-48424600	Enhancers	Brain Hippocampus Middle	brain
2	chr2:48422000-48425200	Enhancers	Brain Substantia Nigra	brain
3	chr2:48422000-48426400	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr2:48422400-48424000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:48422400-48424600	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr2:48422600-48424400	Weak transcription	Lung	lung
7	chr2:48422600-48425000	Enhancers	Fetal Muscle Leg	muscle
8	chr2:48423200-48424000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr2:48423200-48424000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr2:48423200-48424000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr2:48423200-48424000	Enhancers	Brain Cingulate Gyrus	brain
12	chr2:48423200-48424000	Enhancers	Fetal Intestine Large	intestine
13	chr2:48423200-48424000	Enhancers	Stomach Mucosa	stomach
14	chr2:48423200-48424200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr2:48423200-48424200	Enhancers	Fetal Brain Male	brain
16	chr2:48423200-48424600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr2:48423200-48424600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:48423200-48424600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:48423200-48424600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:48423200-48424600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:48423200-48424600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr2:48423200-48424600	Enhancers	Brain Anterior Caudate	brain
23	chr2:48423200-48424600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:48423200-48424600	Enhancers	Fetal Muscle Trunk	muscle
25	chr2:48423200-48424600	Enhancers	Placenta	Placenta
26	chr2:48423200-48424600	Enhancers	HSMM	muscle
27	chr2:48423200-48424600	Enhancers	HSMMtube	muscle
28	chr2:48423200-48425600	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr2:48423200-48426800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr2:48423400-48424000	Enhancers	H9 Cell Line	embryonic stem cell
31	chr2:48423400-48424000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:48423400-48424000	Enhancers	Spleen	Spleen
33	chr2:48423400-48424200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr2:48423400-48424600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:48423400-48424600	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr2:48423400-48424600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:48423400-48424600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr2:48423400-48424800	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr2:48423400-48425000	Enhancers	Liver	Liver
40	chr2:48423400-48425000	Enhancers	Gastric	stomach
41	chr2:48423400-48425200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:48423400-48425400	Enhancers	Adipose Nuclei	Adipose
43	chr2:48423400-48426600	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr2:48423400-48428200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr2:48423600-48424000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:48423600-48424000	Bivalent Enhancer	HepG2	liver
47	chr2:48423600-48424400	Weak transcription	Pancreas	Pancrea
48	chr2:48423600-48424400	Weak transcription	Right Ventricle	heart
49	chr2:48423600-48424600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:48423600-48424600	Enhancers	Brain Angular Gyrus	brain

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