Variant report

Variant	rs6442122
Chromosome Location	chr3:48498295-48498296
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	chr3:48486865..48488473-chr3:48496764..48498435,2	MCF-7	breast:
2	chr3:48489543..48493797-chr3:48496122..48499063,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164053	Chromatin interaction
ENSG00000244380	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10780032	1.00[EUR][1000 genomes]
rs11130169	1.00[EUR][1000 genomes]
rs11915428	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12633518	1.00[YRI][hapmap]
rs3924179	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858818	1.00[EUR][1000 genomes]
rs55782175	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58835493	1.00[EUR][1000 genomes]
rs59352296	1.00[EUR][1000 genomes]
rs60352528	1.00[EUR][1000 genomes]
rs6762888	0.93[YRI][hapmap]
rs6791777	1.00[EUR][1000 genomes]
rs6793732	1.00[EUR][1000 genomes]
rs6801348	1.00[EUR][1000 genomes]
rs73830466	1.00[EUR][1000 genomes]
rs73830478	1.00[EUR][1000 genomes]
rs73831562	1.00[EUR][1000 genomes]
rs73831565	1.00[EUR][1000 genomes]
rs73831572	1.00[EUR][1000 genomes]
rs73831577	1.00[EUR][1000 genomes]
rs73831579	1.00[EUR][1000 genomes]
rs7633433	1.00[EUR][1000 genomes]
rs898226	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9852211	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9917799	1.00[EUR][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	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48489200-48498800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr3:48489200-48506200	Weak transcription	Stomach Mucosa	stomach
3	chr3:48489200-48507400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:48489400-48498600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:48489400-48500200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:48489400-48500200	Weak transcription	Colonic Mucosa	Colon
7	chr3:48489400-48500800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:48489600-48500600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:48489600-48506400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:48489800-48506600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:48490400-48498400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:48491000-48503200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:48491400-48503000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:48491400-48503000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:48491400-48503200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:48491400-48503200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:48491400-48506600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:48491600-48500400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:48491600-48502600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:48491600-48503000	Strong transcription	Adipose Nuclei	Adipose
21	chr3:48491600-48503200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:48491800-48503200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:48491800-48506400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:48492000-48499200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:48492000-48500200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:48492000-48500200	Strong transcription	Placenta	Placenta
27	chr3:48492000-48503200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:48492000-48503200	Strong transcription	Liver	Liver
29	chr3:48492000-48503600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:48492200-48503200	Strong transcription	Thymus	Thymus
31	chr3:48492200-48503400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:48492200-48503400	Strong transcription	Fetal Stomach	stomach
33	chr3:48492400-48499400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:48492400-48500200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:48492400-48502800	Strong transcription	Lung	lung
36	chr3:48492400-48503000	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr3:48492400-48503000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr3:48492600-48501800	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:48492600-48503000	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:48492600-48503000	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:48492600-48503000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:48492600-48503000	Strong transcription	Brain Germinal Matrix	brain
43	chr3:48492600-48503000	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr3:48492600-48503200	Strong transcription	Primary T cells from cord blood	blood
45	chr3:48492600-48503200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:48492600-48503200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:48492600-48503200	Strong transcription	Dnd41	blood
48	chr3:48492600-48503400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr3:48492600-48503600	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr3:48492600-48504400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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