Variant report

Variant	rs57908018
Chromosome Location	chr6:2435332-2435333
allele	A/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	TEAD4	chr6:2433675-2435640	ECC-1	luminal epithelium:	n/a	n/a
2	NR3C1	chr6:2435134-2435440	ECC-1	luminal epithelium:	n/a	chr6:2435244-2435251
3	TCF12	chr6:2433745-2435613	ECC-1	luminal epithelium:	n/a	chr6:2435355-2435363 chr6:2434823-2434830
4	NFIC	chr6:2433647-2436143	ECC-1	luminal epithelium:	n/a	n/a
5	ESR1	chr6:2435095-2435567	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr6:2435059-2435524	ECC-1	luminal epithelium:	n/a	n/a
7	TCF12	chr6:2435039-2435602	ECC-1	luminal epithelium:	n/a	chr6:2435355-2435363
8	ESR1	chr6:2435108-2435457	ECC-1	luminal epithelium:	n/a	n/a
9	NFIC	chr6:2435027-2435618	ECC-1	luminal epithelium:	n/a	n/a
10	MAX	chr6:2433848-2435486	ECC-1	luminal epithelium:	n/a	chr6:2434783-2434792 chr6:2434782-2434791 chr6:2434782-2434791 chr6:2434777-2434796
11	EP300	chr6:2433679-2435728	ECC-1	luminal epithelium:	n/a	chr6:2434486-2434493

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:2435125..2436735-chr6:2441414..2444146,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf195-19	chr6:2435149-2435586	NONHSAT106669

Variant related genes	Relation type
ENSG00000272465	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11964241	0.87[AMR][1000 genomes]
rs28633763	0.87[AMR][1000 genomes]
rs4602753	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59455919	0.87[AMR][1000 genomes]
rs60798809	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6901457	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6904942	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6905100	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6905118	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6909863	1.00[AMR][1000 genomes]
rs6929207	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73344778	0.87[AMR][1000 genomes]
rs73344794	0.87[AMR][1000 genomes]
rs73344796	0.87[AMR][1000 genomes]
rs73346609	0.87[AMR][1000 genomes]
rs73346610	0.87[AMR][1000 genomes]
rs73346620	0.87[AMR][1000 genomes]
rs73346662	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73346668	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73346669	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73346702	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73348609	1.00[AMR][1000 genomes]
rs7739140	0.87[AMR][1000 genomes]
rs7744661	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2399800-2449200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:2402200-2449200	Weak transcription	Left Ventricle	heart
3	chr6:2414600-2452000	Weak transcription	Ovary	ovary
4	chr6:2414800-2448800	Weak transcription	Liver	Liver
5	chr6:2414800-2449200	Weak transcription	Fetal Stomach	stomach
6	chr6:2417600-2454200	Weak transcription	Pancreas	Pancrea
7	chr6:2426400-2439800	Weak transcription	Aorta	Aorta
8	chr6:2428800-2446200	Weak transcription	Right Ventricle	heart
9	chr6:2431400-2435400	Enhancers	HMEC	breast
10	chr6:2431600-2439800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:2431800-2435800	Enhancers	Esophagus	oesophagus
12	chr6:2432200-2435400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:2432200-2449200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:2433200-2449200	Weak transcription	Adipose Nuclei	Adipose
15	chr6:2433400-2437200	Weak transcription	HSMM	muscle
16	chr6:2433600-2447000	Weak transcription	Fetal Intestine Large	intestine
17	chr6:2434000-2437000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:2434000-2437600	Enhancers	Fetal Kidney	kidney
19	chr6:2434000-2448400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:2434200-2442600	Weak transcription	Lung	lung
21	chr6:2434400-2449200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:2434600-2439800	Weak transcription	Spleen	Spleen
23	chr6:2434800-2435400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr6:2434800-2435800	Enhancers	Fetal Muscle Leg	muscle
25	chr6:2434800-2436000	Weak transcription	Placenta	Placenta
26	chr6:2434800-2436400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:2435000-2435800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:2435000-2436000	Enhancers	Fetal Muscle Trunk	muscle
29	chr6:2435000-2436400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:2435000-2437000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:2435000-2449200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:2435200-2435400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr6:2435200-2435600	Weak transcription	Fetal Intestine Small	intestine
34	chr6:2435200-2435600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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