Variant report

Variant	rs1543680
Chromosome Location	chr6:26103177-26103178
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr6:26102745-26103452	K562	blood:	n/a	n/a
2	REST	chr6:26103171-26104855	H1-neurons	neurons:	n/a	n/a
3	MYBL2	chr6:26103173-26105760	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26102660..26104205-chr6:27804912..27807560,2	MCF-7	breast:
2	chr6:26101409..26106036-chr6:27098701..27102040,8	K562	blood:
3	chr6:26103055..26105911-chr6:27113369..27117045,6	K562	blood:
4	chr17:56708534..56710943-chr6:26103089..26104740,2	MCF-7	breast:
5	chr6:26052762..26068184-chr6:26093226..26113078,68	MCF-7	breast:
6	chr6:26042662..26045122-chr6:26102656..26104697,2	MCF-7	breast:
7	chr6:26101462..26104336-chr6:26520946..26522887,2	MCF-7	breast:
8	chr15:71407014..71408733-chr6:26102615..26104813,2	MCF-7	breast:
9	chr6:26019620..26034082-chr6:26100355..26110400,33	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H4C	TF binding region
ENSG00000196226	Chromatin interaction
ENSG00000184348	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000234816	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000225362	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000184825	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10484432	0.92[CHB][hapmap];0.96[CHD][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];0.87[ASN][1000 genomes]
rs10946805	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150663	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12192649	1.00[LWK][hapmap];1.00[MEX][hapmap]
rs12199626	0.87[ASN][1000 genomes]
rs12204800	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12205050	0.88[ASN][1000 genomes]
rs16891325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16891344	0.84[ASN][1000 genomes]
rs1773284	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1773285	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2009610	1.00[MEX][hapmap]
rs2032444	0.88[CHD][hapmap]
rs2229768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2858996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35276045	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs41266791	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59306177	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6931542	0.83[ASN][1000 genomes]
rs707889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707890	0.96[ASN][1000 genomes]
rs707891	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs707892	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs707893	0.87[ASN][1000 genomes]
rs707894	0.87[ASN][1000 genomes]
rs707896	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs707898	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs707899	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs806976	0.83[ASN][1000 genomes]
rs8384	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[EUR][1000 genomes];0.91[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	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
8	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1543680	U91328.19	cis	Nerve Tibial	GTEx
rs1543680	U91328.19	cis	Muscle Skeletal	GTEx
rs1543680	U91328.19	cis	Esophagus Mucosa	GTEx
rs1543680	HIST1H2AI	cis	parietal	SCAN
rs1543680	ZNF391	cis	cerebellum	SCAN
rs1543680	HIST1H1C	cis	parietal	SCAN
rs1543680	U91328.19	cis	Thyroid	GTEx
rs1543680	U91328.19	cis	Heart Left Ventricle	GTEx
rs1543680	U91328.19	cis	Artery Tibial	GTEx
rs1543680	U91328.19	cis	Adipose Subcutaneous	GTEx
rs1543680	HIST1H3H	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26088400-26104000	Weak transcription	Esophagus	oesophagus
2	chr6:26089000-26103200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:26089200-26103200	Weak transcription	Fetal Lung	lung
4	chr6:26089200-26103400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:26089200-26103400	Weak transcription	Right Atrium	heart
6	chr6:26089600-26103200	Weak transcription	HMEC	breast
7	chr6:26089800-26103200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:26089800-26103200	Weak transcription	Fetal Stomach	stomach
9	chr6:26089800-26103400	Weak transcription	Fetal Intestine Large	intestine
10	chr6:26089800-26103400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:26089800-26103600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:26089800-26103600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:26090000-26103200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:26090000-26104200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:26090200-26103400	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:26090400-26103200	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:26090400-26103400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:26091800-26103200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:26091800-26103400	Weak transcription	Placenta	Placenta
20	chr6:26091800-26103400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:26091800-26103400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:26092000-26103400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:26093200-26103400	Weak transcription	GM12878-XiMat	blood
24	chr6:26093200-26104200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:26093400-26103400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr6:26093600-26103200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:26093800-26103200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:26093800-26103400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:26094000-26103400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:26094800-26103400	Weak transcription	Adipose Nuclei	Adipose
31	chr6:26095000-26103400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:26095200-26103200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:26099600-26104200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:26102200-26103400	Enhancers	Fetal Thymus	thymus
35	chr6:26102600-26103200	Enhancers	A549	lung
36	chr6:26102600-26103200	Enhancers	Dnd41	blood
37	chr6:26102600-26103200	Enhancers	NHEK	skin
38	chr6:26102600-26104000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr6:26102800-26103200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:26102800-26103200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:26102800-26103200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr6:26102800-26103200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:26102800-26103200	Enhancers	Hela-S3	cervix
44	chr6:26102800-26103200	Enhancers	HepG2	liver
45	chr6:26102800-26103200	Enhancers	K562	blood
46	chr6:26102800-26103200	Enhancers	NH-A	brain
47	chr6:26102800-26103200	Enhancers	NHLF	lung
48	chr6:26102800-26103200	Enhancers	Osteobl	bone
49	chr6:26102800-26103400	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr6:26102800-26103400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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