Variant report

Variant	rs3798542
Chromosome Location	chr6:34522772-34522773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34426702..34428652-chr6:34520960..34523550,2	MCF-7	breast:
2	chr6:34204520..34207436-chr6:34522666..34524361,2	K562	blood:
3	chr6:32936553..32938765-chr6:34521756..34523748,2	MCF-7	breast:
4	chr6:34435937..34438924-chr6:34520705..34523320,2	MCF-7	breast:
5	chr18:50300436..50303454-chr6:34521553..34523812,3	MCF-7	breast:
6	chr6:34205000..34207351-chr6:34521778..34524214,3	MCF-7	breast:
7	chr6:34522438..34524089-chr6:34549801..34552822,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204256	Chromatin interaction
ENSG00000221635	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000137309	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10947510	0.86[ASN][1000 genomes]
rs3756929	0.96[EUR][1000 genomes]
rs3756930	0.93[EUR][1000 genomes]
rs3756931	0.96[EUR][1000 genomes]
rs3798541	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800463	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713812	0.91[EUR][1000 genomes]
rs4713813	0.91[EUR][1000 genomes]
rs4713815	0.90[EUR][1000 genomes]
rs4713817	0.91[EUR][1000 genomes]
rs6901672	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296119	0.96[EUR][1000 genomes]
rs9296120	0.96[EUR][1000 genomes]
rs9296121	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription 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	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv885786	chr6:34426884-34542662	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
7	esv1813536	chr6:34455242-34545123	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	nsv885787	chr6:34458533-34546560	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
9	nsv885788	chr6:34464010-34551912	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
10	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	38 gene(s)	inside rSNPs	diseases
11	nsv885789	chr6:34474939-34546560	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
12	nsv885790	chr6:34483015-34542662	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
13	nsv885791	chr6:34483015-34546560	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
14	nsv516578	chr6:34483015-34561585	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
15	esv1801907	chr6:34492567-34545860	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
16	nsv1016788	chr6:34496002-34529165	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
17	nsv885792	chr6:34507311-34607958	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
18	nsv1023870	chr6:34509776-34544041	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
19	nsv1015306	chr6:34509776-34549107	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
20	nsv1032763	chr6:34509776-34552797	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
21	nsv1025472	chr6:34509776-34555969	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
22	nsv1021859	chr6:34515436-34535289	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
23	nsv1033534	chr6:34516588-34555969	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
24	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34513200-34524000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:34515200-34527600	Weak transcription	Right Atrium	heart
3	chr6:34520800-34523000	Enhancers	Fetal Thymus	thymus
4	chr6:34521000-34523000	Weak transcription	Fetal Lung	lung
5	chr6:34521200-34522800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:34521400-34523000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:34521400-34523000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr6:34521400-34523000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:34521400-34523000	Enhancers	K562	blood
10	chr6:34521800-34523000	Flanking Active TSS	A549	lung
11	chr6:34521800-34523200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr6:34522000-34522800	Flanking Active TSS	Fetal Stomach	stomach
13	chr6:34522000-34523000	Enhancers	Fetal Muscle Leg	muscle
14	chr6:34522000-34524400	Active TSS	Fetal Intestine Large	intestine
15	chr6:34522200-34524000	Active TSS	Fetal Intestine Small	intestine
16	chr6:34522400-34523000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:34522400-34523200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:34522400-34523800	Enhancers	Lung	lung
19	chr6:34522400-34524000	Active TSS	Rectal Smooth Muscle	rectum
20	chr6:34522400-34524400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:34522400-34527400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:34522600-34522800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:34522600-34522800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:34522600-34522800	Active TSS	Colonic Mucosa	Colon
25	chr6:34522600-34523000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr6:34522600-34523000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr6:34522600-34524200	Active TSS	Gastric	stomach
28	chr6:34522600-34524200	Active TSS	Stomach Mucosa	stomach

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