Variant report

Variant	rs6442104
Chromosome Location	chr3:48181928-48181929
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48173560..48176129-chr3:48181769..48183974,2	MCF-7	breast:
2	chr3:48129466..48131531-chr3:48181644..48184632,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000047849	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2593817	1.00[AMR][1000 genomes]
rs319683	1.00[AMR][1000 genomes]
rs34675858	1.00[AMR][1000 genomes]
rs3731495	1.00[AMR][1000 genomes]
rs3731539	1.00[AMR][1000 genomes]
rs3731547	1.00[AMR][1000 genomes]
rs4476528	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55808934	1.00[AMR][1000 genomes]
rs6442092	1.00[AMR][1000 genomes]
rs6773945	1.00[AMR][1000 genomes]
rs7372108	1.00[AMR][1000 genomes]
rs73831540	1.00[AMR][1000 genomes]
rs73831544	1.00[AMR][1000 genomes]
rs73831562	1.00[AMR][1000 genomes]
rs73831565	1.00[AMR][1000 genomes]
rs9863220	1.00[AMR][1000 genomes]
rs9917799	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv1012828	chr3:47996472-48192862	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats 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 target site	17 gene(s)	inside rSNPs	diseases
7	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv876760	chr3:48019258-48197614	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv1012024	chr3:48119229-48242670	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv834682	chr3:48138137-48311122	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 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	chr3:48172400-48184000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:48172800-48184000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:48179600-48182800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:48179600-48183000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:48179800-48183000	Weak transcription	NHEK	skin
6	chr3:48181600-48182200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:48181600-48184200	Enhancers	Fetal Muscle Leg	muscle
8	chr3:48181600-48185800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr3:48181800-48182000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:48181800-48182000	Enhancers	Adipose Nuclei	Adipose
11	chr3:48181800-48182000	Enhancers	HMEC	breast
12	chr3:48181800-48182200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr3:48181800-48182200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr3:48181800-48182200	Enhancers	H1 Cell Line	embryonic stem cell
15	chr3:48181800-48182200	Enhancers	H9 Cell Line	embryonic stem cell
16	chr3:48181800-48182200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:48181800-48182200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:48181800-48182200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:48181800-48182200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr3:48181800-48182200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr3:48181800-48182200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr3:48181800-48182200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr3:48181800-48182200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:48181800-48182200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:48181800-48182200	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr3:48181800-48182200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:48181800-48182200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:48181800-48182200	Enhancers	Duodenum Mucosa	Duodenum
29	chr3:48181800-48182200	Enhancers	Fetal Heart	heart
30	chr3:48181800-48182200	Flanking Active TSS	Fetal Kidney	kidney
31	chr3:48181800-48182200	Enhancers	Placenta	Placenta
32	chr3:48181800-48182200	Enhancers	Ovary	ovary
33	chr3:48181800-48182200	Enhancers	Pancreas	Pancrea
34	chr3:48181800-48182200	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr3:48181800-48182200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr3:48181800-48182200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr3:48181800-48182200	Flanking Active TSS	HepG2	liver
38	chr3:48181800-48182200	Flanking Active TSS	HUVEC	blood vessel
39	chr3:48181800-48182200	Enhancers	K562	blood
40	chr3:48181800-48182400	Enhancers	Right Ventricle	heart
41	chr3:48181800-48182600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:48181800-48183000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:48181800-48183400	Enhancers	Fetal Muscle Trunk	muscle
44	chr3:48181800-48184400	Enhancers	Left Ventricle	heart
45	chr3:48181800-48184400	Enhancers	Lung	lung
46	chr3:48181800-48184600	Enhancers	Esophagus	oesophagus
47	chr3:48181800-48185000	Enhancers	Spleen	Spleen

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