Variant report

Variant	rs41378047
Chromosome Location	chr1:46602011-46602012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46601377..46603890-chr1:46611538..46613763,2	MCF-7	breast:
2	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
3	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:
4	chr1:46595304..46602065-chr1:46660247..46665309,8	MCF-7	breast:
5	chr1:46600538..46602719-chr1:109690592..109692888,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085998	Chromatin interaction
ENSG00000250719	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000117472	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17102066	1.00[AMR][1000 genomes]
rs2275425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28363193	1.00[AMR][1000 genomes]
rs4297232	1.00[AMR][1000 genomes]
rs57121950	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57959845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57991520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58888694	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59669845	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59768249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59919818	1.00[AMR][1000 genomes]
rs59974520	1.00[AMR][1000 genomes]
rs60411062	1.00[AMR][1000 genomes]
rs60789947	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60933200	1.00[AMR][1000 genomes]
rs61178863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1012418	chr1:46544842-46619890	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv534948	chr1:46544842-46619890	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46599200-46603200	Weak transcription	Ovary	ovary
2	chr1:46599400-46602200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:46599400-46603200	Weak transcription	Liver	Liver
4	chr1:46599600-46603200	Weak transcription	HSMMtube	muscle
5	chr1:46599600-46604000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:46599800-46603200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:46600000-46602400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:46600000-46602400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:46600000-46602600	Weak transcription	Fetal Kidney	kidney
10	chr1:46600000-46603200	Weak transcription	HUVEC	blood vessel
11	chr1:46600000-46604000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:46600200-46603200	Weak transcription	Fetal Intestine Large	intestine
13	chr1:46600200-46603200	Weak transcription	Fetal Lung	lung
14	chr1:46600400-46602200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:46600400-46602200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:46600400-46602400	Weak transcription	Aorta	Aorta
17	chr1:46600400-46602400	Weak transcription	Right Atrium	heart
18	chr1:46600600-46602200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:46600600-46603400	Weak transcription	HSMM	muscle
20	chr1:46600800-46602400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:46600800-46602600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:46601000-46602200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:46601000-46602200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:46601000-46603000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:46601000-46603200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:46601000-46603200	Weak transcription	Adipose Nuclei	Adipose
27	chr1:46601000-46603200	Weak transcription	NHLF	lung
28	chr1:46601000-46603400	Weak transcription	K562	blood
29	chr1:46601000-46603400	Weak transcription	NH-A	brain
30	chr1:46601200-46602200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:46601200-46603000	Enhancers	Fetal Heart	heart
32	chr1:46601200-46603200	Weak transcription	Fetal Stomach	stomach
33	chr1:46601200-46603400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:46601400-46602800	Enhancers	Brain Germinal Matrix	brain
35	chr1:46601400-46603200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:46601400-46603200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:46601400-46603200	Weak transcription	Osteobl	bone
38	chr1:46601400-46603400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:46601400-46603600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:46601600-46602400	Weak transcription	Fetal Muscle Leg	muscle
41	chr1:46601600-46602400	Weak transcription	Left Ventricle	heart
42	chr1:46601600-46602600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr1:46601600-46603200	Enhancers	Hela-S3	cervix
44	chr1:46601800-46603200	Weak transcription	Fetal Muscle Trunk	muscle

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