Variant report

Variant	rs2559602
Chromosome Location	chr12:106530161-106530162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:106426879..106427562-chr12:106529618..106530330,2	MCF-7	breast:
2	chr12:105814363..105815481-chr12:106529622..106530636,3	MCF-7	breast:
3	chr12:106425864..106426522-chr12:106529759..106530547,2	MCF-7	breast:
4	chr12:106197861..106199984-chr12:106529644..106531234,2	MCF-7	breast:
5	chr12:106389362..106391020-chr12:106528296..106530507,2	MCF-7	breast:
6	chr12:106099358..106100248-chr12:106529662..106530556,3	K562	blood:
7	chr12:106164560..106166544-chr12:106529852..106531635,2	MCF-7	breast:
8	chr12:105814176..105815093-chr12:106530126..106530769,2	MCF-7	breast:
9	chr12:106480275..106482643-chr12:106529582..106531677,2	MCF-7	breast:
10	chr12:106529633..106530327-chr12:106598845..106599811,3	MCF-7	breast:
11	chr12:106425879..106426591-chr12:106529828..106530360,2	MCF-7	breast:
12	chr12:106099637..106100474-chr12:106529654..106530671,3	MCF-7	breast:
13	chr12:106529953..106533456-chr12:106589507..106592473,3	MCF-7	breast:
14	chr12:106168262..106170732-chr12:106528906..106531408,2	MCF-7	breast:
15	chr12:105848787..105849764-chr12:106529532..106530649,7	MCF-7	breast:
16	chr12:106168956..106169805-chr12:106529679..106530573,5	MCF-7	breast:
17	chr12:105814165..105815073-chr12:106529681..106530596,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000074590	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1215597	0.80[ASW][hapmap];0.92[CEU][hapmap];0.80[CHB][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2434081	0.86[ASN][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	nsv1040534	chr12:106528394-106619175	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2559602	ELAVL4	trans	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106504800-106532400	Weak transcription	Spleen	Spleen
2	chr12:106509800-106531400	Weak transcription	Gastric	stomach
3	chr12:106520600-106530200	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr12:106524200-106530200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr12:106524400-106530600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:106525200-106530200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:106525600-106530200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr12:106525600-106530200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:106525600-106530200	Enhancers	H9 Cell Line	embryonic stem cell
10	chr12:106525800-106530400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:106526600-106531200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:106526600-106531600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr12:106527200-106530200	Enhancers	HepG2	liver
14	chr12:106527200-106530600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:106528000-106530200	Enhancers	Fetal Muscle Trunk	muscle
16	chr12:106528000-106530800	Enhancers	Placenta	Placenta
17	chr12:106528200-106530200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr12:106528400-106530400	Transcr. at gene 5' and 3'	HSMMtube	muscle
19	chr12:106528600-106530800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:106528600-106534200	Active TSS	Fetal Brain Female	brain
21	chr12:106528800-106530200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr12:106528800-106531600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:106528800-106531600	Flanking Active TSS	NH-A	brain
24	chr12:106528800-106532400	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr12:106529000-106530200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:106529000-106530600	Flanking Active TSS	Right Atrium	heart
27	chr12:106529000-106531400	Flanking Active TSS	HUVEC	blood vessel
28	chr12:106529000-106532600	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr12:106529200-106530200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:106529200-106530200	Weak transcription	Lung	lung
31	chr12:106529200-106530200	Weak transcription	Pancreas	Pancrea
32	chr12:106529200-106531200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:106529200-106534200	Active TSS	Right Ventricle	heart
34	chr12:106529200-106534600	Active TSS	Aorta	Aorta
35	chr12:106529200-106535000	Active TSS	Left Ventricle	heart
36	chr12:106529400-106531400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:106529400-106534000	Active TSS	Ovary	ovary
38	chr12:106529600-106530200	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr12:106529600-106530600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:106529600-106530800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr12:106529600-106530800	Flanking Active TSS	NHLF	lung
42	chr12:106529600-106531800	Flanking Active TSS	HMEC	breast
43	chr12:106529600-106532000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:106529600-106532000	Flanking Active TSS	NHEK	skin
45	chr12:106529600-106533800	Active TSS	HSMM	muscle
46	chr12:106529600-106535000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:106529800-106530200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
48	chr12:106529800-106530200	Active TSS	Brain Cingulate Gyrus	brain
49	chr12:106529800-106530200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
50	chr12:106529800-106530200	Enhancers	Fetal Kidney	kidney

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