Variant report

Variant	rs59893653
Chromosome Location	chr6:128759755-128759756
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	chr6:128748805..128750318-chr6:128759354..128761042,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10428737	0.89[EUR][1000 genomes]
rs17055854	0.89[EUR][1000 genomes]
rs17459362	0.95[EUR][1000 genomes]
rs1891146	0.89[EUR][1000 genomes]
rs1891147	0.89[EUR][1000 genomes]
rs1891148	0.87[EUR][1000 genomes]
rs58395468	0.89[EUR][1000 genomes]
rs66843622	0.89[EUR][1000 genomes]
rs6939023	0.95[EUR][1000 genomes]
rs722796	0.89[EUR][1000 genomes]
rs72974018	0.84[EUR][1000 genomes]
rs72974042	0.80[EUR][1000 genomes]
rs72974046	0.89[EUR][1000 genomes]
rs72974053	0.89[EUR][1000 genomes]
rs72974060	0.89[EUR][1000 genomes]
rs72974074	0.89[EUR][1000 genomes]
rs72974081	0.81[EUR][1000 genomes]
rs961292	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128739800-128762600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:128740800-128777000	Weak transcription	Fetal Intestine Small	intestine
3	chr6:128753200-128777000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:128754800-128761200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:128754800-128767000	Weak transcription	NHEK	skin
6	chr6:128756400-128776600	Weak transcription	Fetal Intestine Large	intestine
7	chr6:128758200-128763600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:128758600-128760200	Enhancers	Brain Substantia Nigra	brain
9	chr6:128758600-128763800	Weak transcription	Stomach Mucosa	stomach
10	chr6:128758800-128759800	Enhancers	Left Ventricle	heart
11	chr6:128758800-128760000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr6:128758800-128760000	Enhancers	Ovary	ovary
13	chr6:128758800-128761200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr6:128758800-128766600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:128759000-128759800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:128759000-128759800	Enhancers	Right Ventricle	heart
17	chr6:128759000-128760000	Enhancers	H9 Cell Line	embryonic stem cell
18	chr6:128759000-128760000	Enhancers	Fetal Thymus	thymus
19	chr6:128759000-128760200	Enhancers	H1 Cell Line	embryonic stem cell
20	chr6:128759000-128760200	Enhancers	Fetal Brain Male	brain
21	chr6:128759000-128760200	Enhancers	Fetal Heart	heart
22	chr6:128759000-128760400	Enhancers	Brain Hippocampus Middle	brain
23	chr6:128759200-128759800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:128759200-128759800	Enhancers	Gastric	stomach
25	chr6:128759200-128759800	Enhancers	Pancreas	Pancrea
26	chr6:128759200-128760000	Enhancers	Stomach Smooth Muscle	stomach
27	chr6:128759200-128760200	Enhancers	Brain Cingulate Gyrus	brain
28	chr6:128759200-128760200	Enhancers	Colon Smooth Muscle	Colon
29	chr6:128759200-128760800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:128759200-128761000	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr6:128759200-128763000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr6:128759400-128759800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:128759400-128759800	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr6:128759400-128759800	Enhancers	HMEC	breast
35	chr6:128759400-128760000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:128759400-128760000	Enhancers	Fetal Muscle Leg	muscle
37	chr6:128759400-128760200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:128759400-128760200	Enhancers	Brain Anterior Caudate	brain
39	chr6:128759400-128760400	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr6:128759400-128761400	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr6:128759400-128761400	Enhancers	Thymus	Thymus
42	chr6:128759400-128765000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:128759600-128759800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:128759600-128760000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr6:128759600-128760000	Enhancers	Esophagus	oesophagus
46	chr6:128759600-128760000	Enhancers	Fetal Brain Female	brain
47	chr6:128759600-128760000	Enhancers	Fetal Stomach	stomach
48	chr6:128759600-128760000	Enhancers	Right Atrium	heart
49	chr6:128759600-128760000	Enhancers	HUVEC	blood vessel
50	chr6:128759600-128760200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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