Variant report

Variant	rs977598
Chromosome Location	chr4:75037867-75037868
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:75032536..75034809-chr4:75036870..75039307,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10008940	0.83[EUR][1000 genomes]
rs10026869	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10028397	0.82[EUR][1000 genomes]
rs10938111	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12163831	1.00[CEU][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes]
rs12646785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1265346	0.97[ASN][1000 genomes]
rs13116686	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13136363	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1440407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16850531	1.00[CEU][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes]
rs16850541	0.94[EUR][1000 genomes]
rs2289443	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[EUR][1000 genomes]
rs28823933	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4694183	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs479409	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs510884	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs518475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs519014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533352	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs535753	0.84[ASN][1000 genomes]
rs537061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538542	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs538775	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs547975	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551906	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564793	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6446975	1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824352	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs977597	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv594683	chr4:75013441-75106485	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1013260	chr4:75013441-75121643	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1002907	chr4:75013441-75131443	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1004706	chr4:75014770-75121643	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv594684	chr4:75015750-75106485	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75024800-75056600	Weak transcription	Pancreas	Pancrea
2	chr4:75024800-75080600	Weak transcription	Left Ventricle	heart
3	chr4:75025000-75046800	Weak transcription	NHDF-Ad	bronchial
4	chr4:75025200-75041800	Weak transcription	Aorta	Aorta
5	chr4:75025200-75042600	Weak transcription	Brain Substantia Nigra	brain
6	chr4:75025400-75067600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:75025400-75073600	Weak transcription	Right Ventricle	heart
8	chr4:75025600-75054200	Weak transcription	Ovary	ovary
9	chr4:75025600-75067600	Weak transcription	Thymus	Thymus
10	chr4:75025800-75049200	Weak transcription	Psoas Muscle	Psoas
11	chr4:75026800-75049200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:75027200-75044400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:75027600-75046600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr4:75027800-75049200	Weak transcription	Adipose Nuclei	Adipose
15	chr4:75027800-75054600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr4:75028000-75039200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:75028200-75040800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:75028200-75042600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:75028200-75067600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:75028400-75042800	Weak transcription	Fetal Heart	heart
21	chr4:75028600-75040600	Weak transcription	Fetal Thymus	thymus
22	chr4:75028600-75044000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:75028600-75047000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:75028600-75051200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:75028800-75072800	Weak transcription	Liver	Liver
26	chr4:75029000-75041400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:75029000-75046400	Weak transcription	Primary B cells from cord blood	blood
28	chr4:75030800-75040600	Weak transcription	Primary T cells from cord blood	blood
29	chr4:75030800-75040800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:75030800-75046400	Weak transcription	HSMM	muscle
31	chr4:75030800-75055200	Weak transcription	NHEK	skin
32	chr4:75030800-75055800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:75031600-75040400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:75032200-75045200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:75034200-75039200	Weak transcription	K562	blood
36	chr4:75034200-75071800	Weak transcription	HMEC	breast
37	chr4:75035000-75041200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr4:75037800-75048600	Weak transcription	Brain Anterior Caudate	brain

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