Variant report

Variant	rs1416289
Chromosome Location	chr6:140297603-140297604
allele	A/G
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	chr6:139693777..139697007-chr6:140297471..140300569,5	MCF-7	breast:
2	chr6:140297195..140299311-chr6:140303038..140305448,2	K562	blood:
3	chr6:140296686..140298552-chr6:140300622..140302808,2	K562	blood:
4	chr6:139697609..139700104-chr6:140295382..140298304,2	MCF-7	breast:
5	chr6:140259128..140260901-chr6:140296853..140299455,2	MCF-7	breast:
6	chr6:139693589..139696606-chr6:140296332..140298975,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HECA-3	chr6:140296929-140297930	NONHSAT115266

No data

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1028469	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10434888	0.87[CEU][hapmap]
rs10872525	0.87[CEU][hapmap]
rs12175776	0.82[EUR][1000 genomes]
rs12525047	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12526885	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12663217	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12663483	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665399	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194747	0.87[EUR][1000 genomes]
rs13194827	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204837	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17069768	0.87[CEU][hapmap]
rs1933742	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1953788	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1953789	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs586246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs587235	0.90[CHB][hapmap];0.82[JPT][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs592056	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs598498	0.85[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs616279	0.90[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs618515	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs622216	0.96[ASN][1000 genomes]
rs62429515	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62429516	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62429517	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs647968	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs648510	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs650774	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs67013338	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs679849	0.86[CHB][hapmap];0.82[JPT][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs680290	0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs681235	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6926807	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6928433	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724061	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743656	0.88[ASN][1000 genomes]
rs7758187	0.87[CEU][hapmap]
rs856646	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9373255	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9373256	0.87[CEU][hapmap]
rs9373259	0.93[CEU][hapmap]
rs9376482	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9376485	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9376494	0.87[CEU][hapmap]
rs9385888	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9385895	0.87[CEU][hapmap]
rs9385902	0.87[CEU][hapmap]
rs9385903	0.93[CEU][hapmap]
rs9389733	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9389741	0.87[CEU][hapmap]
rs9399298	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9399299	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9399304	0.81[CEU][hapmap]
rs9399308	0.93[CEU][hapmap]
rs9403134	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403135	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9403148	0.87[CEU][hapmap]
rs9495636	0.88[YRI][hapmap]
rs9495641	0.88[YRI][hapmap]

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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140287800-140299000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:140291600-140302000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:140292600-140306000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:140294200-140299400	Enhancers	Fetal Heart	heart
5	chr6:140295200-140299000	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:140295200-140303000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:140295400-140298000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:140295400-140298600	Weak transcription	A549	lung
9	chr6:140295400-140298800	Weak transcription	HSMMtube	muscle
10	chr6:140295400-140300400	Weak transcription	Fetal Kidney	kidney
11	chr6:140295400-140300400	Weak transcription	Fetal Stomach	stomach
12	chr6:140295400-140300400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:140295400-140301800	Weak transcription	Aorta	Aorta
14	chr6:140295400-140302000	Weak transcription	Adipose Nuclei	Adipose
15	chr6:140295400-140302800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:140295400-140303000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:140295600-140298200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:140295600-140298600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:140295600-140298800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:140295600-140299000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:140295600-140302000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:140295600-140302600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:140295600-140303400	Weak transcription	Right Atrium	heart
24	chr6:140295800-140298600	Weak transcription	HSMM	muscle
25	chr6:140295800-140298800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:140295800-140298800	Weak transcription	NH-A	brain
27	chr6:140295800-140299000	Weak transcription	HUVEC	blood vessel
28	chr6:140295800-140299000	Weak transcription	K562	blood
29	chr6:140296000-140298200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:140296400-140298200	Weak transcription	Hela-S3	cervix
31	chr6:140296400-140298800	Weak transcription	Osteobl	bone
32	chr6:140296400-140302600	Weak transcription	Fetal Lung	lung
33	chr6:140296600-140298200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:140296600-140298200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:140296600-140298400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr6:140297000-140299000	Enhancers	Placenta	Placenta
37	chr6:140297000-140299600	Enhancers	NHDF-Ad	bronchial
38	chr6:140297000-140301800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:140297200-140298800	Weak transcription	NHLF	lung
40	chr6:140297200-140299400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:140297400-140298600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:140297400-140305800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:140297600-140297800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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