Variant report

Variant	rs9469041
Chromosome Location	chr6:31680205-31680206
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:113)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:113 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:31680200-31680350	GM12868	blood:	n/a	n/a
2	CTCF	chr6:31680168-31680339	GM19239	blood:	n/a	n/a
3	CTCF	chr6:31680052-31680427	T-47D	breast:	n/a	n/a
4	CTCF	chr6:31680160-31680310	HPF	lung:	n/a	n/a
5	POLR2A	chr6:31680068-31680609	MCF-7	breast:	n/a	n/a
6	CTCF	chr6:31680097-31680418	NHEK	skin:	n/a	n/a
7	CTCF	chr6:31680182-31680351	HUVEC	blood vessel:	n/a	n/a
8	CTCF	chr6:31680180-31680330	HEEpiC	esophagus:	n/a	n/a
9	MYC	chr6:31680192-31680282	MCF-7	breast:	n/a	n/a
10	CTCF	chr6:31680130-31680380	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr6:31680200-31680350	AG04449	skin:	n/a	n/a
12	CTCF	chr6:31680180-31680330	GM12872	blood:	n/a	n/a
13	CTCF	chr6:31680138-31680364	ProgFib	skin:	n/a	n/a
14	CTCF	chr6:31680140-31680290	GM12871	blood:	n/a	n/a
15	CTCF	chr6:31680180-31680330	GM12874	blood:	n/a	n/a
16	RAD21	chr6:31680113-31680336	SK-N-SH_RA	brain:	n/a	n/a
17	CTCF	chr6:31680060-31680504	MCF-7	breast:	n/a	n/a
18	CTCF	chr6:31680160-31680310	GM06990	blood:	n/a	n/a
19	RAD21	chr6:31679979-31680546	HCT-116	colon:	n/a	n/a
20	CTCF	chr6:31680200-31680350	AG09309	skin:	n/a	n/a
21	CTCF	chr6:31680200-31680350	GM12867	blood:	n/a	n/a
22	CTCF	chr6:31680180-31680330	GM12864	blood:	n/a	n/a
23	CTCF	chr6:31680200-31680350	MCF-7	breast:	n/a	n/a
24	RAD21	chr6:31680036-31680573	MCF-7	breast:	n/a	n/a
25	MYC	chr6:31680149-31680349	MCF-7	breast:	n/a	n/a
26	CTCF	chr6:31680200-31680350	HCT-116	colon:	n/a	n/a
27	SMC3	chr6:31680133-31680391	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr6:31680200-31680350	RPTEC	kidney:	n/a	n/a
29	MYC	chr6:31680100-31680363	MCF-7	breast:	n/a	n/a
30	CTCF	chr6:31680160-31680310	A549	lung:	n/a	n/a
31	CTCF	chr6:31680200-31680350	HRPEpiC	eye:	n/a	n/a
32	CTCF	chr6:31680160-31680310	SK-N-SH_RA	brain:	n/a	n/a
33	CTCF	chr6:31680196-31680315	GM19240	blood:	n/a	n/a
34	RAD21	chr6:31680125-31680372	A549	lung:	n/a	n/a
35	CTCF	chr6:31680160-31680310	GM12873	blood:	n/a	n/a
36	CTCF	chr6:31680200-31680350	HEEpiC	esophagus:	n/a	n/a
37	CTCF	chr6:31680160-31680310	AG04449	skin:	n/a	n/a
38	CTCF	chr6:31680181-31680341	Pancreas_OC	pancreas:	n/a	n/a
39	CTCF	chr6:31680109-31680407	MCF-7	breast:	n/a	n/a
40	CTCF	chr6:31680200-31680350	NHEK	skin:	n/a	n/a
41	CTCF	chr6:31680180-31680330	HBMEC	blood vessel:	n/a	n/a
42	CTCF	chr6:31680160-31680310	HRPEpiC	eye:	n/a	n/a
43	CTCF	chr6:31680180-31680330	HA-sp	spinal cord:	n/a	n/a
44	CTCF	chr6:31680120-31680270	GM12869	blood:	n/a	n/a
45	CTCF	chr6:31680171-31680345	GM12891	blood:	n/a	n/a
46	EBF1	chr6:31680100-31680342	GM12878	blood:	n/a	n/a
47	CTCF	chr6:31680122-31680391	Gliobla	brain:	n/a	n/a
48	RAD21	chr6:31680132-31680385	Hela-S3	cervix:	n/a	n/a
49	ZKSCAN1	chr6:31680147-31680296	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr6:31680120-31680270	GM12864	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31670633..31671925-chr6:31679998..31680724,3	MCF-7	breast:
2	chr6:31679533..31681521-chr6:31865296..31867225,2	MCF-7	breast:
3	chr6:31632238..31634263-chr6:31678523..31680253,2	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:
6	chr6:31680166..31680692-chr6:31697407..31698330,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LY6G6E.7-1	chr6:31680118-31680338	NR_003673

No data

Variant related genes	Relation type
LY6G6D	TF binding region
ENSG00000204427	Chromatin interaction
ENSG00000213722	Chromatin interaction
ENSG00000166278	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000204371	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12181589	1.00[EUR][1000 genomes]
rs9296002	1.00[EUR][1000 genomes]
rs9461715	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461727	1.00[EUR][1000 genomes]
rs9469031	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469032	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469043	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469057	1.00[EUR][1000 genomes]
rs9469059	1.00[EUR][1000 genomes]
rs9469062	1.00[EUR][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:45 , 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	chr6:31677800-31680600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:31678400-31680400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:31678400-31683200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr6:31678400-31684200	Enhancers	Fetal Brain Male	brain
11	chr6:31678800-31681200	Weak transcription	Thymus	Thymus
12	chr6:31679000-31680400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:31679000-31681200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:31679000-31681600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:31679200-31680400	Weak transcription	Fetal Intestine Large	intestine
16	chr6:31679200-31681200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:31679200-31681200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:31679200-31681200	Weak transcription	Fetal Intestine Small	intestine
19	chr6:31679200-31681600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:31679200-31683600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:31679200-31687800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:31679400-31680600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:31679400-31681400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:31679400-31681600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:31679400-31681600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:31679400-31691200	Weak transcription	Primary B cells from cord blood	blood
27	chr6:31679600-31680400	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr6:31679600-31680600	Enhancers	Esophagus	oesophagus
29	chr6:31679600-31680800	Enhancers	NHEK	skin
30	chr6:31679600-31681600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr6:31679800-31680400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:31679800-31681400	Bivalent Enhancer	HepG2	liver
33	chr6:31679800-31681800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:31680000-31680400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:31680000-31680400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:31680000-31680400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:31680000-31681600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr6:31680000-31683600	Enhancers	Fetal Thymus	thymus
39	chr6:31680200-31680600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:31680200-31680600	Flanking Active TSS	Fetal Brain Female	brain
41	chr6:31680200-31680800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:31680200-31681600	Weak transcription	Placenta	Placenta
43	chr6:31680200-31681800	Weak transcription	Stomach Mucosa	stomach
44	chr6:31680200-31682400	Enhancers	Primary T cells from cord blood	blood
45	chr6:31680200-31685200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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