Variant report

Variant	rs9396240
Chromosome Location	chr6:56816979-56816980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr6:56816648-56817036	K562	blood:	n/a	n/a
2	ZNF143	chr6:56816791-56817026	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56816669..56821714-chr6:56908406..56912975,10	K562	blood:
2	chr6:56815308..56817719-chr6:56918047..56920182,2	K562	blood:

Variant related genes	Relation type
BEND6	TF binding region
ENSG00000168116	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1007417	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1016048	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10498814	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12175661	0.96[EUR][1000 genomes]
rs13205191	0.96[EUR][1000 genomes]
rs1562908	0.85[CHD][hapmap]
rs1597694	0.99[ASN][1000 genomes]
rs16888268	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17685356	0.99[ASN][1000 genomes]
rs17758527	0.96[EUR][1000 genomes]
rs17758663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1839837	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006930	0.99[ASN][1000 genomes]
rs2008698	1.00[ASN][1000 genomes]
rs2306011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2397227	0.85[CHD][hapmap]
rs28498151	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34589109	0.96[ASN][1000 genomes]
rs34703235	0.94[ASN][1000 genomes]
rs34896907	0.97[ASN][1000 genomes]
rs35553446	1.00[ASN][1000 genomes]
rs4576249	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs57994994	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58099889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58332182	0.88[EUR][1000 genomes]
rs59106338	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60401134	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60910121	0.92[EUR][1000 genomes]
rs62411412	0.88[EUR][1000 genomes]
rs62411417	0.92[EUR][1000 genomes]
rs62411418	0.92[EUR][1000 genomes]
rs62411419	0.92[EUR][1000 genomes]
rs62411420	0.96[EUR][1000 genomes]
rs62411421	0.96[EUR][1000 genomes]
rs62411422	0.96[EUR][1000 genomes]
rs62411423	0.96[EUR][1000 genomes]
rs62411425	0.96[EUR][1000 genomes]
rs62411430	0.96[EUR][1000 genomes]
rs62417377	0.96[EUR][1000 genomes]
rs62417378	0.94[EUR][1000 genomes]
rs62417384	1.00[ASN][1000 genomes]
rs62417385	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62417410	0.99[ASN][1000 genomes]
rs6901192	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6901660	0.99[ASN][1000 genomes]
rs6904172	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6915492	0.99[ASN][1000 genomes]
rs6924882	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6935636	0.99[ASN][1000 genomes]
rs720885	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7760435	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9349842	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9357936	0.96[EUR][1000 genomes]
rs9367700	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367702	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370552	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9370553	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9370554	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9382669	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9382670	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9382673	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382674	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9382675	0.99[ASN][1000 genomes]
rs9396238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9396245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396246	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9396249	0.99[ASN][1000 genomes]
rs9396251	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9396252	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9396254	0.96[EUR][1000 genomes]
rs9464411	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475757	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475758	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9475760	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9475761	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9475762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475763	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56804200-56818000	Weak transcription	HSMM	muscle
2	chr6:56806600-56817800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:56806600-56818000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:56806600-56818400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:56810000-56818200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:56812600-56817400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:56813000-56817400	Weak transcription	Hela-S3	cervix
8	chr6:56813200-56818200	Weak transcription	HSMMtube	muscle
9	chr6:56813600-56817000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:56813600-56817600	Weak transcription	HMEC	breast
11	chr6:56814200-56817200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:56814600-56818200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:56814800-56818400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:56815200-56818600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:56815400-56817600	Weak transcription	Brain Substantia Nigra	brain
16	chr6:56815400-56818200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:56815600-56817600	Weak transcription	Brain Angular Gyrus	brain
18	chr6:56815600-56817800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:56815600-56818000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:56815800-56818200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:56816000-56817400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:56816000-56817800	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:56816000-56817800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
24	chr6:56816000-56818000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:56816000-56818200	Weak transcription	HUVEC	blood vessel
26	chr6:56816200-56817400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:56816200-56817400	Weak transcription	K562	blood
28	chr6:56816200-56817600	Weak transcription	Brain Anterior Caudate	brain
29	chr6:56816200-56817800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr6:56816200-56817800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:56816200-56817800	Weak transcription	NHEK	skin
32	chr6:56816200-56818000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:56816200-56818000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:56816600-56817200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:56816600-56817200	Enhancers	GM12878-XiMat	blood
36	chr6:56816600-56817400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr6:56816600-56817400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:56816600-56817400	Weak transcription	A549	lung
39	chr6:56816800-56817000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:56816800-56817000	Flanking Active TSS	NHLF	lung
41	chr6:56816800-56817000	Genic enhancers	Osteobl	bone
42	chr6:56816800-56817400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:56816800-56817800	Weak transcription	NH-A	brain

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