Variant report

Variant	rs6570399
Chromosome Location	chr6:140859280-140859281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:140858084..140862104-chr6:140862610..140866313,5	MCF-7	breast:
2	chr6:140859129..140859897-chr8:105520075..105520755,2	MCF-7	breast:
3	chr6:140858927..140861812-chr6:141885115..141886624,2	MCF-7	breast:
4	chr6:139694080..139696813-chr6:140857145..140860019,3	MCF-7	breast:
5	chr6:140762424..140765135-chr6:140858930..140861399,3	MCF-7	breast:
6	chr6:140773150..140776945-chr6:140859067..140862028,3	MCF-7	breast:
7	chr6:140857240..140860582-chr6:140860847..140863194,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12523675	0.87[EUR][1000 genomes]
rs12524116	0.81[EUR][1000 genomes]
rs17069962	0.87[EUR][1000 genomes]
rs17069974	0.93[EUR][1000 genomes]
rs17070037	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60481239	0.83[EUR][1000 genomes]
rs60510685	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6570397	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs955446	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv817390	chr6:140558103-141166039	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv432965	chr6:140692307-140866307	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv886694	chr6:140701423-141001420	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1029179	chr6:140733884-141051309	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1018932	chr6:140779526-140863146	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1021431	chr6:140779526-140865994	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv2763973	chr6:140779538-140863146	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1029847	chr6:140798377-140928132	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv538451	chr6:140798377-140928132	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1031320	chr6:140798377-141156979	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
12	nsv604771	chr6:140801497-140895423	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1026042	chr6:140813667-141414842	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1034469	chr6:140818729-140908576	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1020190	chr6:140818729-140910627	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv2761069	chr6:140818741-141099004	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
17	nsv1025422	chr6:140819415-140910627	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv869287	chr6:140826709-141407102	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
19	nsv604772	chr6:140827025-140890348	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
20	nsv604773	chr6:140829464-140902819	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv1034376	chr6:140844320-140981566	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv521860	chr6:140849702-140911389	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv1032510	chr6:140849815-140908576	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv1026713	chr6:140859250-140904356	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv1032561	chr6:140859250-140908576	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv1033576	chr6:140859250-140910627	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140856400-140860200	Weak transcription	Left Ventricle	heart
2	chr6:140857200-140861000	Enhancers	NHLF	lung
3	chr6:140857600-140860400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:140858200-140860400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:140858200-140860400	Enhancers	Rectal Smooth Muscle	rectum
6	chr6:140858400-140859400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:140858400-140859400	Enhancers	Placenta	Placenta
8	chr6:140858400-140859400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr6:140858400-140859400	Enhancers	HSMMtube	muscle
10	chr6:140858400-140859600	Enhancers	Colon Smooth Muscle	Colon
11	chr6:140858400-140859600	Enhancers	Fetal Kidney	kidney
12	chr6:140858400-140859800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr6:140858400-140859800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:140858400-140859800	Enhancers	Fetal Lung	lung
15	chr6:140858400-140860000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr6:140858400-140860000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:140858400-140860200	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr6:140858400-140860400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:140858400-140860400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr6:140858400-140860400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:140858400-140860400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:140858400-140860400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:140858400-140861000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:140858600-140859400	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr6:140858600-140859800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:140858600-140859800	Active TSS	A549	lung
27	chr6:140858600-140860200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr6:140858600-140860200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr6:140858600-140860400	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr6:140858600-140860400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr6:140858600-140860400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr6:140858800-140859400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:140858800-140859400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:140858800-140859400	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr6:140858800-140859400	Flanking Active TSS	Psoas Muscle	Psoas
36	chr6:140858800-140859400	Flanking Active TSS	HMEC	breast
37	chr6:140858800-140859600	Enhancers	Stomach Mucosa	stomach
38	chr6:140858800-140859600	Enhancers	Hela-S3	cervix
39	chr6:140858800-140860000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:140858800-140860000	Enhancers	Fetal Brain Female	brain
41	chr6:140858800-140860000	Enhancers	HUVEC	blood vessel
42	chr6:140858800-140860200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr6:140859000-140859400	Enhancers	H1 Cell Line	embryonic stem cell
44	chr6:140859000-140859400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr6:140859000-140859400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:140859000-140859400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:140859000-140859400	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr6:140859000-140859400	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr6:140859000-140859400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:140859000-140859400	Enhancers	Fetal Muscle Leg	muscle

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