Variant report

Variant	rs4296677
Chromosome Location	chr4:6946208-6946209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:6916306..6918370-chr4:6943424..6946324,3	K562	blood:
2	chr4:6944446..6947031-chr4:6951567..6953686,2	K562	blood:
3	chr4:6917668..6920987-chr4:6945472..6948090,3	K562	blood:
4	chr4:6941810..6943426-chr4:6944150..6946769,2	K562	blood:
5	chr4:6909142..6912159-chr4:6946034..6948699,3	K562	blood:
6	chr4:6945003..6947109-chr4:6955850..6957643,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIAA0232-3	chr4:6945338-6947476	NONHSAT095027

No data

Variant related genes	Relation type
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10516181	0.82[ASN][1000 genomes]
rs10937772	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10937774	0.80[EUR][1000 genomes]
rs10937776	0.82[ASN][1000 genomes]
rs11732898	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12510715	0.82[ASN][1000 genomes]
rs12642852	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13108082	0.88[ASN][1000 genomes]
rs13111887	0.88[ASN][1000 genomes]
rs13122119	0.82[ASN][1000 genomes]
rs13135912	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13149411	0.82[ASN][1000 genomes]
rs2359194	0.82[ASN][1000 genomes]
rs34219101	0.88[ASN][1000 genomes]
rs34335938	0.82[ASN][1000 genomes]
rs34463709	0.82[ASN][1000 genomes]
rs34481892	0.82[ASN][1000 genomes]
rs34959511	0.82[ASN][1000 genomes]
rs35170004	0.82[ASN][1000 genomes]
rs3857171	0.82[ASN][1000 genomes]
rs3892490	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4234788	0.88[ASN][1000 genomes]
rs4234791	0.82[ASN][1000 genomes]
rs4428285	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4458452	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4645214	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689059	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4689060	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4689563	0.82[ASN][1000 genomes]
rs4689564	0.82[ASN][1000 genomes]
rs4689565	0.82[ASN][1000 genomes]
rs4689566	0.82[ASN][1000 genomes]
rs4689567	0.82[ASN][1000 genomes]
rs4689568	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4689573	0.82[ASN][1000 genomes]
rs55822670	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66530709	0.82[ASN][1000 genomes]
rs66640699	0.82[ASN][1000 genomes]
rs66931928	0.82[ASN][1000 genomes]
rs66992702	0.82[ASN][1000 genomes]
rs6816660	0.88[ASN][1000 genomes]
rs6816882	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6818744	0.82[ASN][1000 genomes]
rs6831129	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7655563	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7658198	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7661462	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7675524	0.82[ASN][1000 genomes]
rs7693321	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8180337	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][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	nsv878529	chr4:6883012-6983677	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6928000-6969600	Weak transcription	Aorta	Aorta
2	chr4:6934400-6946400	Enhancers	Placenta	Placenta
3	chr4:6939000-6946800	Enhancers	Adipose Nuclei	Adipose
4	chr4:6939200-6947000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:6939200-6947200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr4:6939200-6948000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr4:6939600-6947000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:6940600-6946400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr4:6941400-6946400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:6941400-6946400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:6941400-6947200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr4:6941600-6946800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:6941600-6947000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr4:6941800-6947000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr4:6941800-6947000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr4:6941800-6947800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr4:6942000-6946600	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr4:6942000-6948000	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr4:6942200-6947400	Enhancers	Fetal Intestine Large	intestine
20	chr4:6942400-6947000	Enhancers	Small Intestine	intestine
21	chr4:6942600-6946400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:6942600-6947000	Enhancers	Brain Anterior Caudate	brain
23	chr4:6943000-6946800	Enhancers	Liver	Liver
24	chr4:6943200-6946800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr4:6943200-6947000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:6943200-6947200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr4:6943400-6946600	Enhancers	Fetal Brain Male	brain
28	chr4:6943800-6955400	Weak transcription	Brain Substantia Nigra	brain
29	chr4:6944200-6947200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:6944400-6947000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:6944400-6949800	Weak transcription	Fetal Lung	lung
32	chr4:6944600-6946400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr4:6944600-6946800	Enhancers	NHDF-Ad	bronchial
34	chr4:6944600-6947000	Enhancers	A549	lung
35	chr4:6944600-6947200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr4:6944600-6947800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr4:6944800-6946800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr4:6944800-6947400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:6944800-6955400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:6945000-6947200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr4:6945000-6949000	Genic enhancers	Fetal Intestine Small	intestine
42	chr4:6945000-6949600	Weak transcription	Fetal Kidney	kidney
43	chr4:6945000-6955400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr4:6945000-6970200	Weak transcription	Hela-S3	cervix
45	chr4:6945200-6946400	Weak transcription	Stomach Mucosa	stomach
46	chr4:6945200-6946800	Enhancers	Primary B cells from cord blood	blood
47	chr4:6945200-6946800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr4:6945200-6947000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr4:6945200-6955600	Weak transcription	Fetal Brain Female	brain
50	chr4:6945400-6946400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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