Variant report

Variant	rs4712920
Chromosome Location	chr6:25363049-25363050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25273459..25275757-chr6:25360794..25363480,2	MCF-7	breast:
2	chr6:25360833..25363264-chr6:25364832..25366836,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213972	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10946764	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946765	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215347	0.95[ASN][1000 genomes]
rs1880272	0.86[ASN][1000 genomes]
rs2744235	0.88[ASN][1000 genomes]
rs2744236	0.94[ASN][1000 genomes]
rs4712919	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933419	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25359200-25363600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:25359600-25366000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr6:25359800-25367200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:25360000-25367200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:25360000-25367400	Weak transcription	Lung	lung
6	chr6:25360000-25367400	Weak transcription	Right Atrium	heart
7	chr6:25360400-25363800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr6:25360400-25366000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr6:25360400-25366400	Weak transcription	Gastric	stomach
10	chr6:25360400-25367600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:25360400-25367600	Weak transcription	Pancreas	Pancrea
12	chr6:25360400-25367800	Weak transcription	Brain Germinal Matrix	brain
13	chr6:25360400-25369200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:25360600-25365600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:25360800-25367200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:25360800-25367600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:25360800-25369800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:25361000-25363400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:25361000-25364200	Weak transcription	Fetal Thymus	thymus
20	chr6:25361000-25365000	Weak transcription	Ovary	ovary
21	chr6:25361000-25365600	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:25361000-25367000	Weak transcription	Fetal Intestine Small	intestine
23	chr6:25361000-25367200	Weak transcription	Fetal Intestine Large	intestine
24	chr6:25361000-25367200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:25361000-25367400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:25361000-25369200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:25361000-25369400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:25361000-25369400	Weak transcription	Left Ventricle	heart
29	chr6:25361000-25369800	Weak transcription	Brain Substantia Nigra	brain
30	chr6:25361200-25363400	Weak transcription	Adipose Nuclei	Adipose
31	chr6:25361200-25366400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:25361200-25366600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:25361200-25367200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr6:25361400-25363400	Weak transcription	Fetal Lung	lung
35	chr6:25361400-25365400	Weak transcription	Thymus	Thymus
36	chr6:25362000-25367000	Weak transcription	NHLF	lung
37	chr6:25362000-25367200	Weak transcription	Brain Anterior Caudate	brain
38	chr6:25362200-25363200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:25362400-25363200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr6:25362400-25363800	Enhancers	HMEC	breast
41	chr6:25362600-25363600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:25362600-25364000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:25362600-25367200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr6:25362800-25363200	Enhancers	Aorta	Aorta
45	chr6:25362800-25366400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:25362800-25367600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:25363000-25363400	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr6:25363000-25364000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:25363000-25366000	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr6:25363000-25366400	Weak transcription	NHEK	skin

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