Variant report

Variant	rs6823388
Chromosome Location	chr4:100023999-100024000
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10002449	0.81[EUR][1000 genomes]
rs10084896	1.00[GIH][hapmap];0.81[EUR][1000 genomes]
rs17028370	0.81[EUR][1000 genomes]
rs17028758	1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs28730581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730584	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730596	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730601	0.96[EUR][1000 genomes]
rs28730611	1.00[EUR][1000 genomes]
rs28730617	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730625	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730641	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730643	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730644	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730645	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730646	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28730649	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28894370	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28894371	0.87[EUR][1000 genomes]
rs29001338	1.00[EUR][1000 genomes]
rs29001342	1.00[EUR][1000 genomes]
rs29001346	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs29001348	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4295271	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4499706	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5003497	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55831712	0.81[EUR][1000 genomes]
rs61431883	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323213	0.81[EUR][1000 genomes]
rs62323214	0.81[EUR][1000 genomes]
rs62323216	0.81[EUR][1000 genomes]
rs62323217	0.81[EUR][1000 genomes]
rs62323230	0.81[EUR][1000 genomes]
rs62323231	0.81[EUR][1000 genomes]
rs62323233	0.81[EUR][1000 genomes]
rs62323234	0.81[EUR][1000 genomes]
rs62323235	0.81[EUR][1000 genomes]
rs62323236	0.81[EUR][1000 genomes]
rs62323237	0.81[EUR][1000 genomes]
rs62323238	0.81[EUR][1000 genomes]
rs62323240	0.81[EUR][1000 genomes]
rs62323241	0.81[EUR][1000 genomes]
rs62323242	0.81[EUR][1000 genomes]
rs62323244	0.81[EUR][1000 genomes]
rs62323246	0.81[EUR][1000 genomes]
rs62323247	0.81[EUR][1000 genomes]
rs62323248	0.81[EUR][1000 genomes]
rs62323249	0.81[EUR][1000 genomes]
rs62323250	0.81[EUR][1000 genomes]
rs62323251	0.81[EUR][1000 genomes]
rs62323252	0.81[EUR][1000 genomes]
rs62323253	0.81[EUR][1000 genomes]
rs62323254	0.81[EUR][1000 genomes]
rs62323255	0.81[EUR][1000 genomes]
rs62323256	0.81[EUR][1000 genomes]
rs62323257	0.81[EUR][1000 genomes]
rs62323258	0.81[EUR][1000 genomes]
rs62323259	0.81[EUR][1000 genomes]
rs62325160	0.81[EUR][1000 genomes]
rs62325161	0.81[EUR][1000 genomes]
rs62325182	0.81[EUR][1000 genomes]
rs62325183	0.81[EUR][1000 genomes]
rs62325184	0.81[EUR][1000 genomes]
rs62325185	0.81[EUR][1000 genomes]
rs62325186	0.81[EUR][1000 genomes]
rs62325187	0.81[EUR][1000 genomes]
rs62325188	0.81[EUR][1000 genomes]
rs62325189	0.81[EUR][1000 genomes]
rs62325192	0.81[EUR][1000 genomes]
rs62325193	0.81[EUR][1000 genomes]
rs62325194	0.81[EUR][1000 genomes]
rs62325195	0.81[EUR][1000 genomes]
rs62325196	0.81[EUR][1000 genomes]
rs62325197	0.81[EUR][1000 genomes]
rs62325198	0.81[EUR][1000 genomes]
rs62325199	0.81[EUR][1000 genomes]
rs62325200	0.81[EUR][1000 genomes]
rs62325201	0.81[EUR][1000 genomes]
rs62325202	0.81[EUR][1000 genomes]
rs62325203	0.81[EUR][1000 genomes]
rs62325204	0.81[EUR][1000 genomes]
rs62325205	0.81[EUR][1000 genomes]
rs62325206	0.81[EUR][1000 genomes]
rs62325208	0.81[EUR][1000 genomes]
rs62325209	0.81[EUR][1000 genomes]
rs62325210	0.81[EUR][1000 genomes]
rs62325211	0.81[EUR][1000 genomes]
rs62325212	0.81[EUR][1000 genomes]
rs62325213	0.81[EUR][1000 genomes]
rs62325236	0.81[EUR][1000 genomes]
rs62325237	0.81[EUR][1000 genomes]
rs62325238	0.81[EUR][1000 genomes]
rs62325239	1.00[EUR][1000 genomes]
rs62325240	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325241	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325242	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325245	1.00[EUR][1000 genomes]
rs6532781	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6532792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6819694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6819724	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6822742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6827292	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72897156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72897165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72897167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7667261	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7679102	1.00[EUR][1000 genomes]
rs7681427	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7687322	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7688859	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7699232	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9995869	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS 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	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	esv1849572	chr4:100007243-100024396	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1843227	chr4:100021476-100024396	Weak transcription Enhancers Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1002574	chr4:100023999-100133693	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100011400-100025800	Weak transcription	Esophagus	oesophagus
2	chr4:100011600-100025600	Weak transcription	Primary T cells from cord blood	blood
3	chr4:100012800-100063800	Weak transcription	Aorta	Aorta
4	chr4:100014400-100024000	Weak transcription	HMEC	breast
5	chr4:100020400-100024400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:100020600-100034800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:100020800-100032800	Weak transcription	Fetal Intestine Small	intestine
8	chr4:100020800-100038600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr4:100021000-100032200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:100021000-100041200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:100021400-100025200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:100021600-100024400	Weak transcription	Small Intestine	intestine
13	chr4:100022200-100024000	Weak transcription	Osteobl	bone
14	chr4:100022200-100024200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:100022200-100024600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:100022200-100025400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:100022600-100024800	Weak transcription	Adipose Nuclei	Adipose
18	chr4:100022600-100025000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:100022800-100024000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:100022800-100024000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:100023000-100055600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:100023800-100025800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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