Variant report

Variant	rs12506290
Chromosome Location	chr4:55136132-55136133
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:55135740..55138560-chr4:55139917..55141829,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10028020	0.84[EUR][1000 genomes]
rs1105825	0.85[EUR][1000 genomes]
rs12505491	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508225	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12641563	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644709	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644749	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565669	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565670	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17084051	0.81[ASN][1000 genomes]
rs1800809	0.81[ASN][1000 genomes]
rs1800810	0.80[ASN][1000 genomes]
rs1800812	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1800813	0.81[ASN][1000 genomes]
rs2229307	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307049	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307050	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs28374326	0.85[EUR][1000 genomes]
rs28489067	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28528897	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28600756	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650939	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35597368	0.86[EUR][1000 genomes]
rs4358459	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4368668	0.80[ASN][1000 genomes]
rs4422471	0.81[ASN][1000 genomes]
rs4608869	0.80[ASN][1000 genomes]
rs4635872	0.80[ASN][1000 genomes]
rs4864857	0.81[ASN][1000 genomes]
rs4864858	0.80[ASN][1000 genomes]
rs4864859	0.81[ASN][1000 genomes]
rs4864860	0.81[ASN][1000 genomes]
rs4864861	0.81[ASN][1000 genomes]
rs4864862	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4864863	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4864864	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864865	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56145315	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58435984	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58727676	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61320297	0.81[ASN][1000 genomes]
rs6554163	1.00[JPT][hapmap]
rs67279506	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67388297	0.85[EUR][1000 genomes]
rs67432867	0.81[ASN][1000 genomes]
rs67600360	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836215	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6850748	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6855761	0.85[EUR][1000 genomes]
rs73252942	0.81[ASN][1000 genomes]
rs73252946	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73252948	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73252950	0.82[EUR][1000 genomes]
rs7660560	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673597	0.81[ASN][1000 genomes]
rs7673984	0.81[ASN][1000 genomes]
rs7677751	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7678144	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7679903	0.81[ASN][1000 genomes]
rs7681399	0.81[ASN][1000 genomes]
rs7682912	0.87[JPT][hapmap]
rs7686588	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688997	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689569	0.81[ASN][1000 genomes]
rs7690503	0.81[ASN][1000 genomes]
rs7691129	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698425	0.81[ASN][1000 genomes]
rs890203	0.81[ASN][1000 genomes]
rs9991165	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1004408	chr4:55124471-55179212	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv537099	chr4:55124471-55179212	Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv1001094	chr4:55131860-55189739	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55119000-55138600	Weak transcription	Fetal Intestine Small	intestine
2	chr4:55119400-55148000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:55121000-55147600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:55121000-55153200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:55121200-55147200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:55122400-55142600	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:55124400-55140400	Weak transcription	Placenta	Placenta
8	chr4:55124400-55147800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:55124800-55138600	Weak transcription	NH-A	brain
10	chr4:55125400-55140600	Strong transcription	Ovary	ovary
11	chr4:55126400-55140800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:55127000-55138600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:55127800-55140600	Weak transcription	Left Ventricle	heart
14	chr4:55129200-55139000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:55129200-55142400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr4:55130000-55139000	Weak transcription	Esophagus	oesophagus
17	chr4:55130000-55139000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:55130200-55142800	Weak transcription	Gastric	stomach
19	chr4:55130200-55143000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:55130600-55142400	Weak transcription	Right Ventricle	heart
21	chr4:55131600-55148000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:55131800-55137200	Weak transcription	Spleen	Spleen
23	chr4:55132200-55142200	Weak transcription	Liver	Liver
24	chr4:55132400-55142800	Weak transcription	Adipose Nuclei	Adipose
25	chr4:55133200-55143200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr4:55133400-55143000	Weak transcription	Colonic Mucosa	Colon
27	chr4:55134000-55141000	Weak transcription	Psoas Muscle	Psoas
28	chr4:55134200-55136600	Weak transcription	Fetal Kidney	kidney
29	chr4:55134200-55136800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:55135000-55141400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:55135200-55137200	Weak transcription	Fetal Intestine Large	intestine
32	chr4:55135200-55140000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:55135400-55136200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:55135400-55137000	Weak transcription	Fetal Stomach	stomach
35	chr4:55135400-55138200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:55135400-55138200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:55135600-55136800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:55135600-55137000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr4:55135600-55137000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:55135600-55137000	Weak transcription	Aorta	Aorta
41	chr4:55135600-55137200	Strong transcription	NHDF-Ad	bronchial
42	chr4:55135600-55139800	Strong transcription	Osteobl	bone
43	chr4:55135600-55140400	Weak transcription	Fetal Muscle Leg	muscle
44	chr4:55135600-55140600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:55135600-55142200	Weak transcription	Fetal Brain Male	brain
46	chr4:55135800-55136600	Weak transcription	Fetal Lung	lung
47	chr4:55135800-55136600	Weak transcription	NHLF	lung

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