Variant report

Variant	rs9495620
Chromosome Location	chr6:140299541-140299542
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:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:139693777..139697007-chr6:140297471..140300569,5	MCF-7	breast:
2	chr6:139693406..139696942-chr6:140299260..140302508,7	MCF-7	breast:
3	chr6:140200893..140201775-chr6:140298811..140299586,3	MCF-7	breast:
4	chr6:139695460..139698700-chr6:140298901..140302123,4	K562	blood:
5	chr6:139695460..139697236-chr6:140298539..140301196,4	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CITED2-3	chr6:140299286-140299541	XLOC_005858
2	lnc-HECA-3	chr6:140298266-140299576	NONHSAT115266

No data

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1028467	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12197784	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12202967	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1338692	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547749	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1977739	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2211064	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328001	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4416686	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604289	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570387	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6906538	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7751424	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9495615	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140291600-140302000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:140292600-140306000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:140295200-140303000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:140295400-140300400	Weak transcription	Fetal Kidney	kidney
5	chr6:140295400-140300400	Weak transcription	Fetal Stomach	stomach
6	chr6:140295400-140300400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:140295400-140301800	Weak transcription	Aorta	Aorta
8	chr6:140295400-140302000	Weak transcription	Adipose Nuclei	Adipose
9	chr6:140295400-140302800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:140295400-140303000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:140295600-140302000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:140295600-140302600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:140295600-140303400	Weak transcription	Right Atrium	heart
14	chr6:140296400-140302600	Weak transcription	Fetal Lung	lung
15	chr6:140297000-140299600	Enhancers	NHDF-Ad	bronchial
16	chr6:140297000-140301800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:140297400-140305800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:140298200-140300600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:140298200-140300600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:140298200-140300600	Weak transcription	Left Ventricle	heart
21	chr6:140298200-140303000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:140298200-140303000	Weak transcription	Pancreas	Pancrea
23	chr6:140298200-140305600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:140298200-140306200	Enhancers	Hela-S3	cervix
25	chr6:140298400-140299600	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr6:140298400-140300800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:140298600-140299600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:140298600-140299600	Enhancers	A549	lung
29	chr6:140298600-140299600	Enhancers	HSMM	muscle
30	chr6:140298600-140299600	Enhancers	NHEK	skin
31	chr6:140298600-140301400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:140298800-140299600	Enhancers	Rectal Smooth Muscle	rectum
33	chr6:140298800-140299600	Enhancers	HSMMtube	muscle
34	chr6:140298800-140299800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:140298800-140305800	Enhancers	Osteobl	bone
36	chr6:140298800-140306000	Enhancers	NHLF	lung
37	chr6:140299000-140299600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr6:140299000-140299600	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr6:140299000-140299600	Enhancers	Colon Smooth Muscle	Colon
40	chr6:140299000-140300600	Weak transcription	Placenta	Placenta
41	chr6:140299200-140302000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr6:140299400-140299600	Enhancers	Fetal Intestine Large	intestine
43	chr6:140299400-140300400	Weak transcription	Fetal Heart	heart
44	chr6:140299400-140300600	Weak transcription	K562	blood
45	chr6:140299400-140300600	Weak transcription	NH-A	brain
46	chr6:140299400-140301200	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr6:140299400-140301200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr6:140299400-140301600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:140299400-140301600	Weak transcription	Fetal Intestine Small	intestine
50	chr6:140299400-140301800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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