Variant report

Variant	rs12502559
Chromosome Location	chr4:85875640-85875641
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	chr4:85868885..85870740-chr4:85874876..85876493,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10856852	0.86[TSI][hapmap]
rs11097026	0.81[CEU][hapmap]
rs11097028	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12500519	0.85[EUR][1000 genomes]
rs12501525	0.92[AMR][1000 genomes]
rs12503330	0.87[EUR][1000 genomes]
rs12510410	0.80[EUR][1000 genomes]
rs13118671	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13125323	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13139541	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13141072	0.86[EUR][1000 genomes]
rs1484661	0.90[CEU][hapmap];0.91[AMR][1000 genomes]
rs1508670	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17009317	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17009334	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17009341	0.81[CEU][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap]
rs2046404	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs35190829	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35892581	0.92[EUR][1000 genomes]
rs4376130	0.81[EUR][1000 genomes]
rs4383611	1.00[ASW][hapmap];0.85[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4533765	0.86[TSI][hapmap]
rs4590017	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4624645	0.81[EUR][1000 genomes]
rs55871210	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55912355	0.90[EUR][1000 genomes]
rs56094216	0.89[EUR][1000 genomes]
rs58074983	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531777	0.81[CEU][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap]
rs6531782	0.86[TSI][hapmap]
rs6531783	0.93[ASW][hapmap];0.90[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66965560	0.84[EUR][1000 genomes]
rs67624868	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6815917	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6820517	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6829807	0.95[CEU][hapmap];0.89[MEX][hapmap]
rs6847564	0.94[CEU][hapmap]
rs6847811	0.80[EUR][1000 genomes]
rs71631375	0.89[EUR][1000 genomes]
rs72664928	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72664957	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7654035	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs7661609	0.81[CEU][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs7663580	0.86[TSI][hapmap]
rs7682896	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7690054	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7692223	0.90[CEU][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7694949	0.81[CEU][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs7695054	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7699226	0.81[CEU][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv508295	chr4:85822802-85885027	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12502559	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85845600-85882800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:85849200-85876000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:85851200-85876000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:85860600-85877000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:85864400-85876400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:85864400-85877200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:85865200-85876000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr4:85865200-85886400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:85865800-85885400	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:85866000-85886200	Weak transcription	Fetal Intestine Small	intestine
11	chr4:85866400-85879200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:85866800-85884600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:85867800-85878600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:85869600-85879800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:85869800-85879200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:85870000-85876000	Weak transcription	Left Ventricle	heart
17	chr4:85870200-85876000	Weak transcription	Colon Smooth Muscle	Colon
18	chr4:85870200-85879200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:85870400-85876000	Weak transcription	Fetal Kidney	kidney
20	chr4:85870400-85876000	Weak transcription	Ovary	ovary
21	chr4:85870400-85876000	Weak transcription	Right Atrium	heart
22	chr4:85870400-85879200	Weak transcription	Adipose Nuclei	Adipose
23	chr4:85870400-85880800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr4:85870600-85876400	Weak transcription	Fetal Heart	heart
25	chr4:85871000-85876400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:85871000-85879200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr4:85872000-85886600	Weak transcription	Lung	lung
28	chr4:85873200-85877600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr4:85873200-85879200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr4:85873200-85879200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:85873400-85876000	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:85873400-85876000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr4:85873400-85876200	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr4:85873400-85877200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:85873400-85877200	Weak transcription	Right Ventricle	heart
36	chr4:85873400-85878600	Weak transcription	Stomach Mucosa	stomach
37	chr4:85873400-85879200	Weak transcription	Pancreas	Pancrea
38	chr4:85873400-85879600	Weak transcription	Gastric	stomach
39	chr4:85873400-85886600	Weak transcription	Esophagus	oesophagus
40	chr4:85873600-85878600	Weak transcription	Liver	Liver
41	chr4:85873800-85877200	Weak transcription	Psoas Muscle	Psoas
42	chr4:85873800-85878800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:85873800-85879000	Weak transcription	NH-A	brain
44	chr4:85873800-85880600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:85873800-85884800	Weak transcription	HSMM	muscle
46	chr4:85873800-85885400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr4:85873800-85885800	Weak transcription	Osteobl	bone
48	chr4:85874000-85884600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:85874200-85875800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:85874200-85877000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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