Variant report

Variant	rs55643278
Chromosome Location	chr6:26222888-26222889
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr6:26222749-26226655	H1-neurons	neurons:	n/a	n/a
2	ZNF384	chr6:26222888-26223230	GM12878	blood:	n/a	n/a
3	PBX3	chr6:26222841-26223316	SK-N-SH	brain:	n/a	n/a
4	RUNX3	chr6:26222858-26223307	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26222884..26225206-chr6:27806186..27807804,2	MCF-7	breast:
2	chr15:76196195..76197776-chr6:26222407..26224118,2	MCF-7	breast:
3	chr6:26055362..26057199-chr6:26221388..26224194,2	MCF-7	breast:
4	chr1:153939456..153941344-chr6:26220996..26223363,2	MCF-7	breast:
5	chr6:26222789..26225595-chr6:27100763..27103064,2	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H3E	TF binding region
ENSG00000167196	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000143570	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10452600	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10484436	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753131	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753625	0.85[EUR][1000 genomes]
rs11753655	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754744	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11755210	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11755943	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11757394	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11757754	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758351	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11759904	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341759	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16891378	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16891397	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16891401	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16891405	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16891443	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891446	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891455	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891456	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891466	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891467	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891474	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16891481	0.98[ASN][1000 genomes]
rs17598927	0.83[EUR][1000 genomes]
rs1997768	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2022448	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2050948	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050950	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069018	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2069019	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2069020	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2143345	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143346	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2143347	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2183948	0.84[EUR][1000 genomes]
rs3757135	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41266801	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41266807	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55815656	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55848726	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56186759	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56220351	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56398712	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
8	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
9	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
10	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
11	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
12	nsv1025493	chr6:26026870-26223838	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1001 gene(s)	inside rSNPs	diseases
13	nsv1023979	chr6:26026870-26287399	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1113 gene(s)	inside rSNPs	diseases
14	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
15	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
16	nsv482348	chr6:26082709-26261136	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	799 gene(s)	inside rSNPs	diseases
17	nsv883490	chr6:26172219-26231608	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	316 gene(s)	inside rSNPs	diseases
18	nsv1021294	chr6:26190316-26246784	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	309 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26217600-26224000	Weak transcription	Pancreas	Pancrea
2	chr6:26217800-26225400	Weak transcription	Spleen	Spleen
3	chr6:26218000-26223600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:26218000-26223600	Weak transcription	Right Atrium	heart
5	chr6:26218200-26223000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:26218400-26223200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:26218400-26223200	Weak transcription	Fetal Stomach	stomach
8	chr6:26218400-26223600	Weak transcription	Liver	Liver
9	chr6:26218400-26223800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:26218600-26223000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:26218600-26223000	Weak transcription	Osteobl	bone
12	chr6:26218600-26223200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:26218600-26223200	Weak transcription	NH-A	brain
14	chr6:26218600-26223200	Weak transcription	NHLF	lung
15	chr6:26218600-26223400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:26218600-26223800	Weak transcription	Placenta	Placenta
17	chr6:26218800-26223000	Enhancers	Fetal Thymus	thymus
18	chr6:26219000-26223000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr6:26219000-26223000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:26219000-26223000	Weak transcription	Fetal Intestine Small	intestine
21	chr6:26219200-26223000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr6:26219400-26223000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr6:26219400-26223000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr6:26219400-26223200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:26219400-26223800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:26219600-26223000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:26219600-26223800	Weak transcription	Hela-S3	cervix
28	chr6:26220800-26223200	Weak transcription	Primary B cells from cord blood	blood
29	chr6:26221000-26223000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:26221000-26223600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:26221000-26224000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:26221200-26223000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:26221200-26223000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:26221200-26223000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:26221400-26223000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr6:26222400-26223800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:26222600-26223000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr6:26222600-26223000	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr6:26222600-26223000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:26222600-26223000	Enhancers	GM12878-XiMat	blood
41	chr6:26222600-26223200	Enhancers	Primary T cells fromperipheralblood	blood
42	chr6:26222600-26223200	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr6:26222600-26223200	Enhancers	Fetal Brain Male	brain
44	chr6:26222600-26223400	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr6:26222600-26223400	Enhancers	HMEC	breast
46	chr6:26222600-26223400	Enhancers	HUVEC	blood vessel
47	chr6:26222600-26223600	Enhancers	Primary B cells from peripheral blood	blood
48	chr6:26222600-26223600	Enhancers	Fetal Muscle Leg	muscle
49	chr6:26222800-26223000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:26222800-26223000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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