Variant report

Variant	rs9382669
Chromosome Location	chr6:56818146-56818147
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCLAF1	chr6:56818137-56818833	GM12878	blood:	n/a	chr6:56818176-56818185
2	POLR2A	chr6:56817860-56821003	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:56818137-56819678	GM12878	blood:	n/a	n/a
4	NFIC	chr6:56818104-56818905	GM12878	blood:	n/a	n/a
5	MTA3	chr6:56818140-56819528	GM12878	blood:	n/a	n/a
6	MXI1	chr6:56817851-56821832	SK-N-SH	brain:	n/a	chr6:56820811-56820820 chr6:56819810-56819819
7	MXI1	chr6:56817775-56821104	IMR90	lung:	n/a	chr6:56820811-56820820 chr6:56819810-56819819
8	RCOR1	chr6:56817929-56821128	IMR90	lung:	n/a	n/a
9	ATF2	chr6:56818133-56818874	GM12878	blood:	n/a	n/a
10	CTCF	chr6:56818120-56818270	GM12871	blood:	n/a	n/a
11	CTCF	chr6:56818100-56818250	GM12864	blood:	n/a	n/a
12	RELA	chr6:56817939-56819065	GM18951	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:56818015..56821855-chr6:57180367..57183028,4	K562	blood:
2	chr6:56817930..56821539-chr6:56909452..56912838,6	K562	blood:
3	chr6:56809927..56811973-chr6:56817461..56820564,4	MCF-7	breast:
4	chr6:56816669..56821714-chr6:56908406..56912975,10	K562	blood:
5	chr6:56817813..56820711-chr6:56965881..56967844,2	K562	blood:
6	chr6:56817242..56820030-chr9:96215701..96218251,2	MCF-7	breast:
7	chr6:56817510..56820425-chr6:57182215..57184592,2	K562	blood:
8	chr6:56817882..56819972-chr6:57035811..57037517,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAB23-10	chr6:56817639-56818372	NONHSAT113254

No data

Variant related genes	Relation type
BEND6	TF binding region
ENSG00000226803	Chromatin interaction
ENSG00000112208	Chromatin interaction
ENSG00000112200	Chromatin interaction
ENSG00000146143	Chromatin interaction
ENSG00000188938	Chromatin interaction
ENSG00000168116	Chromatin interaction
ENSG00000200224	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1007417	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1016048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154043	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13193465	0.84[TSI][hapmap]
rs13220575	0.84[TSI][hapmap]
rs1451709	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1562908	0.93[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1597694	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16888268	0.99[ASN][1000 genomes]
rs17685277	0.84[TSI][hapmap]
rs17685356	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17758663	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1839837	1.00[ASN][1000 genomes]
rs2006930	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2008698	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2122958	0.86[CEU][hapmap];0.94[EUR][1000 genomes]
rs2167460	0.81[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs2306011	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2397227	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2817573	0.84[TSI][hapmap]
rs28498151	0.94[ASN][1000 genomes]
rs34589109	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34703235	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34896907	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35553446	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57994994	0.99[ASN][1000 genomes]
rs58099889	0.99[ASN][1000 genomes]
rs59106338	0.94[ASN][1000 genomes]
rs60401134	0.99[ASN][1000 genomes]
rs62417384	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62417385	1.00[ASN][1000 genomes]
rs62417410	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6901192	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6901660	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6901944	0.84[TSI][hapmap]
rs6904172	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs6915492	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6924882	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6925107	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6935636	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs720884	0.84[TSI][hapmap]
rs720885	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7741507	0.99[EUR][1000 genomes]
rs7760435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296855	0.81[MEX][hapmap]
rs9296857	0.92[EUR][1000 genomes]
rs9296859	0.81[EUR][1000 genomes]
rs9349842	0.88[ASN][1000 genomes]
rs9357934	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9367700	1.00[ASN][1000 genomes]
rs9367701	1.00[ASN][1000 genomes]
rs9367702	1.00[ASN][1000 genomes]
rs9370550	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9370552	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9370553	0.99[ASN][1000 genomes]
rs9370554	0.94[ASN][1000 genomes]
rs9382670	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382672	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382673	1.00[ASN][1000 genomes]
rs9382674	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9382675	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9382676	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9396238	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs9396240	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9396245	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9396246	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396249	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9396250	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs9396251	0.94[ASN][1000 genomes]
rs9396252	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9396253	0.81[EUR][1000 genomes]
rs9464411	1.00[ASN][1000 genomes]
rs9464412	1.00[ASN][1000 genomes]
rs9464413	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9475757	1.00[ASN][1000 genomes]
rs9475758	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475760	0.85[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475761	0.96[ASN][1000 genomes]
rs9475762	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9475763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9382669	BEND6	cis	Muscle Skeletal	GTEx
rs9382669	BEND6	cis	lymphoblastoid	seeQTL
rs9382669	BEND6	cis	parietal	SCAN
rs9382669	BEND6	cis	cerebellum	SCAN
rs9382669	BEND6	cis	Heart Left Ventricle	GTEx
rs9382669	BEND6	cis	Artery Tibial	GTEx
rs9382669	BEND6	cis	Esophagus Muscularis	GTEx
rs9382669	BEND6	cis	Thyroid	GTEx
rs9382669	C6orf65	cis	multi-tissue	Pritchard
rs9382669	BEND6	cis	Esophagus Mucosa	GTEx
rs9382669	BEND6	cis	lung	GTEx
rs9382669	DST	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56806600-56818400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:56810000-56818200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:56813200-56818200	Weak transcription	HSMMtube	muscle
4	chr6:56814600-56818200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:56814800-56818400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:56815200-56818600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:56815400-56818200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:56815800-56818200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:56816000-56818200	Weak transcription	HUVEC	blood vessel
10	chr6:56817000-56820600	Active TSS	NHLF	lung
11	chr6:56817200-56818600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:56817400-56818400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:56817400-56818400	Flanking Active TSS	Osteobl	bone
14	chr6:56817400-56819000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:56817600-56818200	Flanking Active TSS	A549	lung
16	chr6:56817600-56818400	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:56817600-56818400	Flanking Active TSS	GM12878-XiMat	blood
18	chr6:56817800-56818200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
19	chr6:56817800-56818200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:56817800-56818200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:56817800-56818200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:56817800-56818200	Active TSS	Brain Hippocampus Middle	brain
23	chr6:56817800-56818200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr6:56817800-56818400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:56817800-56818400	Flanking Active TSS	Brain Substantia Nigra	brain
26	chr6:56817800-56818600	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr6:56817800-56818600	Bivalent/Poised TSS	Fetal Brain Female	brain
28	chr6:56817800-56818800	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr6:56817800-56818800	Flanking Active TSS	NH-A	brain
30	chr6:56817800-56819200	Flanking Active TSS	Hela-S3	cervix
31	chr6:56817800-56819400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
32	chr6:56817800-56821200	Active TSS	NHDF-Ad	bronchial
33	chr6:56818000-56818200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
34	chr6:56818000-56818200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:56818000-56818200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
36	chr6:56818000-56818200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
37	chr6:56818000-56818200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr6:56818000-56818200	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:56818000-56818200	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr6:56818000-56818200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:56818000-56818200	Active TSS	Brain Angular Gyrus	brain
42	chr6:56818000-56818200	Enhancers	Placenta	Placenta
43	chr6:56818000-56818400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
44	chr6:56818000-56818400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
45	chr6:56818000-56818400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
46	chr6:56818000-56818400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:56818000-56818400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr6:56818000-56818400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:56818000-56818600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
50	chr6:56818000-56818600	Enhancers	HepG2	liver

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