Variant report

Variant	rs7641418
Chromosome Location	chr3:142500236-142500237
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142499960..142502376-chr3:142502794..142505025,2	MCF-7	breast:
2	chr3:142313766..142316499-chr3:142498136..142500635,2	K562	blood:

Variant related genes	Relation type
ENSG00000120756	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10049098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10049364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10935469	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12330897	0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs12330901	1.00[AMR][1000 genomes]
rs13320613	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13322816	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13325615	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13434361	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16834067	1.00[AMR][1000 genomes]
rs16852648	1.00[AMR][1000 genomes]
rs16852649	1.00[AMR][1000 genomes]
rs16852658	1.00[AMR][1000 genomes]
rs1916641	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28373594	1.00[AMR][1000 genomes]
rs28460347	1.00[AMR][1000 genomes]
rs28505293	1.00[AMR][1000 genomes]
rs28564963	1.00[AMR][1000 genomes]
rs28572271	1.00[AMR][1000 genomes]
rs28678273	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28728040	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58015805	1.00[AMR][1000 genomes]
rs6798447	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs72988606	1.00[AMR][1000 genomes]
rs72988611	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72988625	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72990716	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72992624	1.00[AMR][1000 genomes]
rs72992644	1.00[AMR][1000 genomes]
rs72992647	1.00[AMR][1000 genomes]
rs72992650	1.00[AMR][1000 genomes]
rs73002086	1.00[AMR][1000 genomes]
rs73002087	1.00[AMR][1000 genomes]
rs7622773	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7637053	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7638554	0.84[AFR][1000 genomes]
rs9289650	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9809475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9810360	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9810606	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9811051	0.91[AFR][1000 genomes]
rs9819681	1.00[AMR][1000 genomes]
rs9823492	0.94[YRI][hapmap]
rs9826191	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9827373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9836232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9837730	0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9839771	1.00[AMR][1000 genomes]
rs9846572	1.00[AMR][1000 genomes]
rs9847616	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9850432	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9863330	1.00[AMR][1000 genomes]
rs9867286	1.00[AMR][1000 genomes]
rs9867886	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9875489	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9877174	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9877670	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9879367	1.00[AMR][1000 genomes]
rs9882985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv518623	chr3:142417070-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142467800-142503400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:142468200-142511000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:142468200-142525200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:142468400-142501400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:142468400-142501400	Weak transcription	HSMM	muscle
6	chr3:142468400-142501600	Weak transcription	Left Ventricle	heart
7	chr3:142468400-142508800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:142468400-142525200	Weak transcription	Fetal Brain Male	brain
9	chr3:142468400-142526800	Weak transcription	NHDF-Ad	bronchial
10	chr3:142468400-142529400	Weak transcription	Brain Germinal Matrix	brain
11	chr3:142468600-142525200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:142468800-142513200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:142470600-142505800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:142472400-142509800	Weak transcription	HepG2	liver
15	chr3:142475000-142527200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:142481600-142501400	Weak transcription	Fetal Stomach	stomach
17	chr3:142484600-142506400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:142487000-142502400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:142487400-142501400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:142487400-142501400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:142487400-142513600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:142487600-142503400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:142487800-142506800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:142488800-142505000	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:142488800-142527000	Weak transcription	Brain Anterior Caudate	brain
26	chr3:142489200-142501400	Weak transcription	Aorta	Aorta
27	chr3:142489800-142501200	Weak transcription	Adipose Nuclei	Adipose
28	chr3:142490000-142503600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:142490200-142529400	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:142490400-142501600	Weak transcription	Ovary	ovary
31	chr3:142490400-142522800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:142490800-142507400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:142491400-142501600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:142491400-142503200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:142492400-142501000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:142495400-142527000	Weak transcription	Brain Angular Gyrus	brain
37	chr3:142496800-142501600	Weak transcription	Small Intestine	intestine
38	chr3:142497600-142501400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:142497600-142509000	Weak transcription	A549	lung
40	chr3:142497600-142514200	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:142498600-142502200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:142498600-142517400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:142498600-142522800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:142498600-142526800	Weak transcription	Osteobl	bone
45	chr3:142498800-142503400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:142499000-142527000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr3:142499400-142547800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:142499600-142501400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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