Variant report

Variant	rs9503170
Chromosome Location	chr6:2397560-2397561
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr6:2397534-2397735	MCF10A-Er-Src	breast:	n/a	chr6:2397580-2397591
2	STAT3	chr6:2397416-2397795	MCF10A-Er-Src	breast:	n/a	chr6:2397580-2397591
3	NFIC	chr6:2397383-2397924	ECC-1	luminal epithelium:	n/a	n/a
4	STAT3	chr6:2397483-2397709	MCF10A-Er-Src	breast:	n/a	chr6:2397580-2397591
5	CTCF	chr6:2397460-2397610	NHDF-neo	bronchial:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:2396597..2398652-chr6:2400293..2401857,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WRNIP1-2	chr6:2397455-2397580	ENSG00000250903
2	lnc-WRNIP1-2	chr6:2397455-2397860	ENSG00000250903
3	lnc-WRNIP1-2	chr6:2397477-2397860	XLOC_005127
4	lnc-WRNIP1-2	chr6:2397455-2397754	NONHSAT106637

Variant related genes	Relation type
GMDS-AS1	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10155673	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10155682	1.00[AMR][1000 genomes]
rs10155748	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11964241	0.89[AMR][1000 genomes]
rs11964259	1.00[AMR][1000 genomes]
rs11964680	1.00[AMR][1000 genomes]
rs28633763	0.89[AMR][1000 genomes]
rs34500504	1.00[AMR][1000 genomes]
rs56714114	1.00[AMR][1000 genomes]
rs57504362	1.00[AMR][1000 genomes]
rs59455919	0.89[AMR][1000 genomes]
rs6925879	1.00[AMR][1000 genomes]
rs73344778	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73344794	0.89[AMR][1000 genomes]
rs73344796	0.89[AMR][1000 genomes]
rs73344799	1.00[AMR][1000 genomes]
rs73346609	0.89[AMR][1000 genomes]
rs73346610	0.89[AMR][1000 genomes]
rs73346620	0.89[AMR][1000 genomes]
rs7739140	0.89[AMR][1000 genomes]
rs7744661	0.89[AMR][1000 genomes]
rs9501832	1.00[AMR][1000 genomes]
rs9501833	1.00[AMR][1000 genomes]
rs9501834	1.00[AMR][1000 genomes]
rs9501835	1.00[AMR][1000 genomes]
rs9503171	1.00[AMR][1000 genomes]
rs9503172	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503173	1.00[AMR][1000 genomes]
rs9503174	1.00[AMR][1000 genomes]
rs9503177	1.00[AMR][1000 genomes]
rs9503178	1.00[AMR][1000 genomes]
rs9503179	1.00[AMR][1000 genomes]
rs9503181	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1016878	chr6:2375784-2680476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv498004	chr6:2380300-3313587	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	163 gene(s)	inside rSNPs	diseases
10	esv2763527	chr6:2390712-2400244	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2383000-2397600	Weak transcription	Gastric	stomach
2	chr6:2383200-2398800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:2387600-2398200	Weak transcription	Ovary	ovary
4	chr6:2389400-2397600	Weak transcription	Pancreas	Pancrea
5	chr6:2389600-2398600	Weak transcription	Esophagus	oesophagus
6	chr6:2390600-2399000	Weak transcription	Fetal Intestine Large	intestine
7	chr6:2391600-2399400	Weak transcription	Primary T cells from cord blood	blood
8	chr6:2392400-2400600	Weak transcription	Aorta	Aorta
9	chr6:2392400-2414400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:2392800-2397600	Weak transcription	Fetal Intestine Small	intestine
11	chr6:2394400-2397600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:2395400-2403800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:2396800-2397800	Enhancers	Spleen	Spleen
14	chr6:2396800-2397800	Flanking Active TSS	HSMMtube	muscle
15	chr6:2396800-2398000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr6:2396800-2398000	Enhancers	Fetal Lung	lung
17	chr6:2396800-2398200	Enhancers	Fetal Muscle Leg	muscle
18	chr6:2396800-2400800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:2396800-2415400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:2397000-2397800	Enhancers	Fetal Brain Female	brain
21	chr6:2397000-2397800	Enhancers	Fetal Heart	heart
22	chr6:2397000-2397800	Enhancers	Fetal Stomach	stomach
23	chr6:2397000-2397800	Enhancers	NH-A	brain
24	chr6:2397000-2398000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:2397000-2398200	Enhancers	HMEC	breast
26	chr6:2397000-2399600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:2397000-2402800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:2397000-2409400	Weak transcription	HepG2	liver
29	chr6:2397200-2397600	Flanking Active TSS	NHLF	lung
30	chr6:2397200-2397800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:2397200-2397800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:2397200-2397800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:2397200-2397800	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr6:2397200-2397800	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr6:2397200-2397800	Active TSS	Brain Substantia Nigra	brain
36	chr6:2397200-2397800	Enhancers	Left Ventricle	heart
37	chr6:2397200-2397800	Flanking Active TSS	NHDF-Ad	bronchial
38	chr6:2397200-2397800	Flanking Active TSS	Osteobl	bone
39	chr6:2397200-2398000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:2397200-2398000	Strong transcription	Liver	Liver
41	chr6:2397200-2398000	Enhancers	Fetal Muscle Trunk	muscle
42	chr6:2397200-2398000	ZNF genes & repeats	Lung	lung
43	chr6:2397200-2410200	Weak transcription	Colon Smooth Muscle	Colon
44	chr6:2397400-2397800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:2397400-2397800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr6:2397400-2397800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:2397400-2397800	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr6:2397400-2397800	Flanking Active TSS	HSMM	muscle
49	chr6:2397400-2398000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:2397400-2398000	Enhancers	Adipose Nuclei	Adipose

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