Variant report

Variant	rs9469040
Chromosome Location	chr6:31679874-31679875
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:31679760-31679910	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:31679533..31681521-chr6:31865296..31867225,2	MCF-7	breast:
2	chr6:31632238..31634263-chr6:31678523..31680253,2	MCF-7	breast:
3	chr6:31677895..31680160-chr6:31702614..31704121,2	MCF-7	breast:
4	chr6:31669599..31672574-chr6:31678491..31681695,4	MCF-7	breast:
5	chr6:31679788..31680730-chr6:31737330..31738173,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LY6G6E.7-1	chr6:31679753-31679892	NR_024541

No data

Variant related genes	Relation type
LY6G6D	TF binding region
ENSG00000263020	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000204371	Chromatin interaction
ENSG00000166278	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000204427	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12177823	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2075787	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2255741	0.81[ASN][1000 genomes]
rs2736158	0.83[ASN][1000 genomes]
rs2736161	0.86[ASN][1000 genomes]
rs2736163	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2736165	0.85[ASN][1000 genomes]
rs2736182	0.85[ASN][1000 genomes]
rs2857696	0.81[ASN][1000 genomes]
rs3749952	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713479	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805258	0.86[ASN][1000 genomes]
rs805264	0.86[ASN][1000 genomes]
rs805266	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805267	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805268	0.86[ASN][1000 genomes]
rs805269	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805270	0.86[ASN][1000 genomes]
rs805272	0.86[ASN][1000 genomes]
rs805283	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs805291	0.93[ASN][1000 genomes]
rs805295	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs805298	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805300	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9296001	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9461717	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461718	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9461719	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9461721	0.89[EUR][1000 genomes]
rs9469042	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9469046	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
12	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
13	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
14	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31671600-31681600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:31671800-31695800	Weak transcription	Right Atrium	heart
3	chr6:31672000-31682800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:31672000-31685400	Weak transcription	Gastric	stomach
5	chr6:31677600-31682400	Enhancers	K562	blood
6	chr6:31677600-31683600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr6:31677800-31680000	Enhancers	Primary hematopoietic stem cells	blood
8	chr6:31677800-31680200	Enhancers	Spleen	Spleen
9	chr6:31677800-31680600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:31678200-31680200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:31678200-31680200	Enhancers	Primary B cells from peripheral blood	blood
12	chr6:31678400-31680200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:31678400-31680400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:31678400-31683200	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr6:31678400-31684200	Enhancers	Fetal Brain Male	brain
16	chr6:31678600-31680200	Enhancers	Placenta	Placenta
17	chr6:31678600-31680200	Enhancers	Stomach Mucosa	stomach
18	chr6:31678800-31680000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr6:31678800-31680000	Weak transcription	Pancreas	Pancrea
20	chr6:31678800-31680200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:31678800-31681200	Weak transcription	Thymus	Thymus
22	chr6:31679000-31680000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr6:31679000-31680400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:31679000-31681200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:31679000-31681600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:31679200-31680000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:31679200-31680200	Weak transcription	Small Intestine	intestine
28	chr6:31679200-31680400	Weak transcription	Fetal Intestine Large	intestine
29	chr6:31679200-31681200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:31679200-31681200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:31679200-31681200	Weak transcription	Fetal Intestine Small	intestine
32	chr6:31679200-31681600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:31679200-31683600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:31679200-31687800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:31679400-31680600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:31679400-31681400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:31679400-31681600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:31679400-31681600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:31679400-31691200	Weak transcription	Primary B cells from cord blood	blood
40	chr6:31679600-31680000	Weak transcription	Fetal Thymus	thymus
41	chr6:31679600-31680400	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr6:31679600-31680600	Enhancers	Esophagus	oesophagus
43	chr6:31679600-31680800	Enhancers	NHEK	skin
44	chr6:31679600-31681600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr6:31679800-31680000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:31679800-31680000	Flanking Active TSS	Fetal Brain Female	brain
47	chr6:31679800-31680200	Weak transcription	Primary T cells from cord blood	blood
48	chr6:31679800-31680400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr6:31679800-31681400	Bivalent Enhancer	HepG2	liver
50	chr6:31679800-31681800	Weak transcription	Duodenum Mucosa	Duodenum

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