Variant report

Variant	rs12650153
Chromosome Location	chr4:126373789-126373790
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	chr4:126363138..126365093-chr4:126372306..126373969,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10010000	1.00[AFR][1000 genomes]
rs10021774	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10025691	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10025821	1.00[AFR][1000 genomes]
rs10031471	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10084893	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10857105	1.00[YRI][hapmap]
rs11098811	0.87[AFR][1000 genomes]
rs11932005	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs11941296	1.00[AFR][1000 genomes]
rs12640965	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs12711125	1.00[MKK][hapmap]
rs13132307	0.89[AFR][1000 genomes]
rs13144799	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs13144803	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1354709	0.87[AFR][1000 genomes]
rs1355159	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1395234	0.89[AFR][1000 genomes]
rs1395243	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1396687	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1506356	0.89[AFR][1000 genomes]
rs1506362	0.87[AFR][1000 genomes]
rs1509298	1.00[LWK][hapmap]
rs1509301	1.00[LWK][hapmap]
rs1553714	1.00[YRI][hapmap]
rs1848579	0.87[AFR][1000 genomes]
rs1912041	0.89[AFR][1000 genomes]
rs1912042	0.89[AFR][1000 genomes]
rs1983117	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2036723	0.89[AFR][1000 genomes]
rs2036724	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2135427	1.00[YRI][hapmap]
rs2135428	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2135429	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2390835	1.00[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2390836	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2390837	0.87[AFR][1000 genomes]
rs2390839	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2390840	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2390841	1.00[YRI][hapmap]
rs2457262	1.00[MKK][hapmap]
rs2893131	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs4508902	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs4585321	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4605670	1.00[AFR][1000 genomes]
rs4834030	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4834032	0.89[AFR][1000 genomes]
rs4834033	0.89[AFR][1000 genomes]
rs4834034	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs4834036	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs4834039	1.00[YRI][hapmap]
rs4834041	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4834043	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4834047	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs4996182	1.00[YRI][hapmap]
rs6534479	0.89[AFR][1000 genomes]
rs6534480	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs6534484	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs6534485	1.00[YRI][hapmap]
rs6814158	0.87[AFR][1000 genomes]
rs6816596	1.00[AFR][1000 genomes]
rs6833240	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6851018	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6851098	1.00[AFR][1000 genomes]
rs7656135	1.00[AFR][1000 genomes]
rs7661810	1.00[AFR][1000 genomes]
rs7667605	1.00[YRI][hapmap]
rs7668690	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7675556	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7683955	1.00[YRI][hapmap]
rs7699122	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs925241	0.89[AFR][1000 genomes]
rs958415	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs958844	1.00[AFR][1000 genomes]
rs958845	1.00[YRI][hapmap]
rs963397	1.00[AFR][1000 genomes]
rs988314	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs988315	0.87[AFR][1000 genomes]
rs988863	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs988933	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs9968423	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9991326	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9995153	0.87[AFR][1000 genomes]
rs9996895	1.00[YRI][hapmap];0.89[AFR][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	nsv1006068	chr4:126103233-126497467	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv830051	chr4:126234895-126403426	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv470070	chr4:126299145-126408586	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:126334600-126390400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr4:126335200-126400800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr4:126342400-126375400	Weak transcription	Right Ventricle	heart
4	chr4:126347800-126382800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:126353600-126377000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:126355000-126399600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:126356000-126391600	Weak transcription	HSMM	muscle
8	chr4:126356400-126414200	Weak transcription	Osteobl	bone
9	chr4:126365600-126375400	Weak transcription	Spleen	Spleen
10	chr4:126367000-126401800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:126367600-126377200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:126368400-126377000	Weak transcription	Psoas Muscle	Psoas
13	chr4:126368800-126375600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:126369000-126378000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:126369000-126382800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:126369600-126374200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr4:126369800-126374200	Strong transcription	Fetal Lung	lung
18	chr4:126370000-126375000	Weak transcription	NHLF	lung
19	chr4:126370600-126373800	Strong transcription	Aorta	Aorta
20	chr4:126370600-126373800	Strong transcription	Fetal Muscle Leg	muscle
21	chr4:126370600-126374000	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr4:126371000-126373800	Strong transcription	Stomach Smooth Muscle	stomach
23	chr4:126371000-126377600	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:126371000-126382400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:126371000-126390600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:126371400-126374200	Strong transcription	Fetal Stomach	stomach
27	chr4:126371400-126374800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:126371800-126374000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:126372000-126374600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:126372000-126376800	Weak transcription	Fetal Kidney	kidney
31	chr4:126372000-126402600	Weak transcription	Adipose Nuclei	Adipose
32	chr4:126372200-126390800	Weak transcription	Fetal Brain Female	brain
33	chr4:126372200-126411200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:126372400-126375000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:126372600-126391200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:126372800-126373800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:126373000-126374000	Active TSS	Brain Substantia Nigra	brain
38	chr4:126373000-126376800	Weak transcription	Fetal Intestine Large	intestine
39	chr4:126373200-126373800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:126373200-126373800	Active TSS	Brain Anterior Caudate	brain
41	chr4:126373200-126373800	Active TSS	Brain Cingulate Gyrus	brain
42	chr4:126373200-126373800	ZNF genes & repeats	Lung	lung
43	chr4:126373200-126374000	Active TSS	Brain Angular Gyrus	brain
44	chr4:126373200-126389800	Weak transcription	Liver	Liver
45	chr4:126373400-126373800	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr4:126373400-126383000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:126373400-126389800	Weak transcription	Ovary	ovary
48	chr4:126373600-126373800	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr4:126373600-126375200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:126373600-126389600	Weak transcription	Left Ventricle	heart

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