Variant report

Variant	rs1125000
Chromosome Location	chr6:26287256-26287257
allele	C/T
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:15)
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	JUN	chr6:26283102-26287746	K562	blood:	n/a	chr6:26285885-26285894 chr6:26285881-26285894
2	STAT1	chr6:26285339-26287351	Hela-S3	cervix:	n/a	chr6:26286961-26286970 chr6:26286962-26286971 chr6:26286959-26286973 chr6:26286956-26286976 chr6:26286962-26286970 chr6:26286956-26286976
3	SREBP2	chr6:26284276-26287755	GM12878	blood:	n/a	n/a
4	HEY1	chr6:26287173-26287470	K562	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26285383..26287322-chr6:26595667..26597252,2	K562	blood:
2	chr6:26285546..26288000-chr6:26593708..26598025,4	K562	blood:
3	chr22:37594612..37596195-chr6:26285298..26287282,2	MCF-7	breast:
4	chr6:26282374..26290542-chr6:27772727..27779446,9	MCF-7	breast:
5	chr6:26284926..26288844-chr6:27112544..27117256,7	MCF-7	breast:
6	chr6:26283553..26288411-chr6:27099109..27103890,9	K562	blood:
7	chr6:26283501..26289776-chr6:27108470..27116413,14	K562	blood:
8	chr6:26285889..26287811-chr6:26576369..26578960,2	K562	blood:
9	chr17:50443509..50445009-chr6:26285795..26287525,2	K562	blood:
10	chr6:26286019..26289232-chr6:26328153..26331757,3	MCF-7	breast:
11	chr6:26286125..26287830-chr6:27780556..27782142,2	K562	blood:
12	chr6:26285002..26288145-chr6:27106372..27109970,3	K562	blood:
13	chr6:26283553..26287733-chr6:27097522..27103890,12	K562	blood:
14	chr6:26280754..26288136-chr6:27109918..27116629,16	MCF-7	breast:
15	chr6:26020607..26022712-chr6:26286327..26288134,2	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H4H	TF binding region
ENSG00000196176	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000133466	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1124999	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11756673	0.84[ASN][1000 genomes]
rs12526215	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2142703	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179152	0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2393592	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2393593	0.88[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34916901	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35310879	0.82[EUR][1000 genomes]
rs3999544	0.96[CEU][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4145910	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4412192	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456712	0.81[EUR][1000 genomes]
rs6899452	0.82[ASN][1000 genomes]
rs6916289	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931391	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6939048	0.84[ASN][1000 genomes]
rs6939589	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6940237	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7450556	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs766406	1.00[JPT][hapmap]
rs766407	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7746807	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7747133	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7748935	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7761298	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7769028	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7771202	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9357004	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9358915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9358917	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366649	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9366651	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9379838	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9379843	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9393690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393692	0.96[CEU][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs9393693	1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9393694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9461242	0.84[ASN][1000 genomes]
rs9467703	0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs989134	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
6	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
7	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
8	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
9	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
10	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
11	nsv601173	chr6:26239404-26322524	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	184 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26285600-26287600	Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr6:26286800-26287400	Enhancers	Fetal Intestine Small	intestine
3	chr6:26286800-26287400	Flanking Active TSS	Dnd41	blood
4	chr6:26286800-26287400	Flanking Active TSS	Hela-S3	cervix
5	chr6:26286800-26287800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:26286800-26288400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:26286800-26290400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:26286800-26292200	Weak transcription	Ovary	ovary
9	chr6:26286800-26294400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:26286800-26295400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:26287000-26287400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr6:26287000-26287600	Transcr. at gene 5' and 3'	K562	blood
13	chr6:26287000-26291600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:26287200-26287400	Enhancers	GM12878-XiMat	blood
15	chr6:26287200-26287400	Enhancers	HepG2	liver
16	chr6:26287200-26288000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr6:26287200-26294400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:26287200-26295600	Weak transcription	A549	lung

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