Variant report

Variant	rs3115669
Chromosome Location	chr6:31619024-31619025
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:122)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
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	POLR2A	chr6:31618987-31619259	HepG2	liver:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:31619002-31619052	HMEC	breast:	n/a
2	chr6:31618987-31619037	MCF10A-Er-Src	breast:	n/a
3	chr6:31618987-31619037	HRPEpiC	eye:	n/a
4	chr6:31618987-31619037	ovcar-3	ovarian:	n/a
5	chr6:31618987-31619037	AG04450	lung:	fetal
6	chr6:31619002-31619052	HL-60	blood:	n/a
7	chr6:31619002-31619052	AG10803	skin:	n/a
8	chr6:31619002-31619052	NHDF-neo	bronchial:	n/a
9	chr6:31619002-31619052	HRE	kidney:	n/a
10	chr6:31618987-31619037	U87	brain:	n/a
11	chr6:31619002-31619052	BE2_C	brain:	n/a
12	chr6:31618987-31619037	SAEC	small airway:	n/a
13	chr6:31619002-31619052	PANC-1	pancreas:	n/a
14	chr6:31618987-31619037	HCT-116	colon:	n/a
15	chr6:31618987-31619037	SK-N-SH_RA	brain:	n/a
16	chr6:31618987-31619037	HL-60	blood:	n/a
17	chr6:31619002-31619052	AoSMC	blood vessel:	n/a
18	chr6:31618987-31619037	GM12878	blood:	n/a
19	chr6:31619002-31619052	PFSK-1	brain:	n/a
20	chr6:31618987-31619037	HPAEpiC	pulmonary alveolar:	n/a
21	chr6:31619002-31619052	H1-hESC	embryonic stem cell:	embryo
22	chr6:31618987-31619037	AG10803	skin:	n/a
23	chr6:31619002-31619052	A549	lung:	n/a
24	chr6:31619002-31619052	HAEpiC	amniotic membrane:	n/a
25	chr6:31619002-31619052	GM12892	blood:	n/a
26	chr6:31618987-31619037	HCM	heart:	n/a
27	chr6:31619002-31619052	GM12878	blood:	n/a
28	chr6:31618987-31619037	GM19239	blood:	n/a
29	chr6:31619002-31619052	HCM	heart:	n/a
30	chr6:31619002-31619052	HRCEpiC	kidney:	n/a
31	chr6:31619002-31619052	GM12891	blood:	n/a
32	chr6:31618987-31619037	GM06990	blood:	n/a
33	chr6:31619002-31619052	CMK	blood:	n/a
34	chr6:31619002-31619052	GM19239	blood:	n/a
35	chr6:31619002-31619052	IMR90	lung:	fetal
36	chr6:31618987-31619037	H1-hESC	embryonic stem cell:	embryo
37	chr6:31618987-31619037	T-47D	breast:	n/a
38	chr6:31618987-31619037	HRE	kidney:	n/a
39	chr6:31619002-31619052	SK-N-SH_RA	brain:	n/a
40	chr6:31618987-31619037	HepG2	liver:	n/a
41	chr6:31618987-31619037	LNCaP	prostate:	n/a
42	chr6:31618987-31619037	AG09319	gingival:	n/a
43	chr6:31619002-31619052	RPTEC	kidney:	n/a
44	chr6:31618987-31619037	HMEC	breast:	n/a
45	chr6:31618987-31619037	MCF-7	breast:	n/a
46	chr6:31619002-31619052	HCF	heart:	n/a
47	chr6:31618987-31619037	PFSK-1	brain:	n/a
48	chr6:31618987-31619037	HCF	heart:	n/a
49	chr6:31618987-31619037	A549	lung:	n/a
50	chr6:31618987-31619037	AG09309	skin:	n/a

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31617566..31622844-chr6:31826455..31835211,65	K562	blood:
2	chr6:31617977..31621822-chr6:31647367..31651078,5	MCF-7	breast:
3	chr6:31618484..31622073-chr6:31864833..31868659,4	K562	blood:
4	chr6:31617566..31630444-chr6:31823885..31836000,84	K562	blood:
5	chr6:31586197..31590294-chr6:31618213..31621899,10	MCF-7	breast:
6	chr6:31590485..31592545-chr6:31618288..31620102,2	MCF-7	breast:
7	chr6:31618191..31620672-chr6:31669780..31672189,2	MCF-7	breast:
8	chr6:31618325..31621676-chr6:31863690..31867276,5	K562	blood:
9	chr6:31507205..31511686-chr6:31618024..31622039,13	K562	blood:
10	chr6:31594287..31597004-chr6:31618520..31620536,2	MCF-7	breast:
11	chr6:31618645..31621732-chr6:31914935..31918984,4	K562	blood:
12	chr6:31618887..31620702-chr6:31843664..31845751,2	MCF-7	breast:
13	chr6:31619018..31621668-chr6:31828535..31831298,4	MCF-7	breast:
14	chr6:31507451..31516055-chr6:31617949..31624791,11	MCF-7	breast:
15	chr17:59488570..59491510-chr6:31618990..31620979,2	MCF-7	breast:
16	chr6:31461147..31462941-chr6:31618531..31620077,2	K562	blood:
17	chr6:31618346..31620951-chr6:31659194..31661993,2	MCF-7	breast:
18	chr6:31507406..31516955-chr6:31615847..31623354,26	K562	blood:
19	chr6:31512553..31516955-chr6:31618753..31622292,7	K562	blood:

No data

Variant related genes	Relation type
APOM	TF binding region
APOM	CpG island
ENSG00000204498	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000204371	Chromatin interaction
ENSG00000213760	Chromatin interaction
ENSG00000234006	Chromatin interaction
ENSG00000204516	Chromatin interaction
ENSG00000243649	Chromatin interaction
ENSG00000204428	Chromatin interaction
ENSG00000204385	Chromatin interaction
ENSG00000166278	Chromatin interaction
ENSG00000254870	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000265236	Chromatin interaction
ENSG00000204427	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000204386	Chromatin interaction
ENSG00000200816	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1043620	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2736177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857594	0.87[EUR][1000 genomes]
rs2857600	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857609	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3115668	0.83[EUR][1000 genomes]
rs3117578	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3130050	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3130068	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3130071	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130487	0.82[EUR][1000 genomes]
rs3130625	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131376	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131377	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9267551	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9267576	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9267658	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	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
13	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
14	nsv462871	chr6:31575276-31632134	Strong transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases
15	nsv601942	chr6:31575276-31632134	Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases
16	nsv884419	chr6:31585000-31632651	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	138 gene(s)	inside rSNPs	diseases
17	nsv884420	chr6:31586827-31632651	Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	138 gene(s)	inside rSNPs	diseases
18	nsv884421	chr6:31588151-31631907	Active TSS Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	129 gene(s)	inside rSNPs	diseases
19	nsv884422	chr6:31592524-31631907	Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	83 gene(s)	inside rSNPs	diseases
20	nsv884424	chr6:31593729-31632651	Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	93 gene(s)	inside rSNPs	diseases
21	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
22	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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31589800-31619400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:31617200-31619400	Weak transcription	Gastric	stomach
3	chr6:31617400-31619200	Weak transcription	Psoas Muscle	Psoas
4	chr6:31617600-31619200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:31617600-31619200	Weak transcription	Brain Angular Gyrus	brain
6	chr6:31617600-31619200	Weak transcription	Spleen	Spleen
7	chr6:31617600-31619400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:31617600-31619400	Weak transcription	Esophagus	oesophagus
9	chr6:31617600-31619400	Weak transcription	Ovary	ovary
10	chr6:31617600-31619400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:31617600-31619600	Weak transcription	Aorta	Aorta
12	chr6:31618000-31619200	Genic enhancers	Primary T cells from cord blood	blood
13	chr6:31618200-31619200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:31618200-31619200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr6:31618400-31619200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:31618400-31619200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:31618400-31619200	Transcr. at gene 5' and 3'	HepG2	liver
18	chr6:31618400-31619200	Genic enhancers	Monocytes-CD14+_RO01746	blood
19	chr6:31618400-31619400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr6:31618400-31619400	Flanking Active TSS	Fetal Brain Female	brain
21	chr6:31618600-31619200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr6:31618600-31619200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:31618600-31619200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:31618600-31619200	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr6:31618600-31619200	Enhancers	Primary hematopoietic stem cells	blood
26	chr6:31618600-31619200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:31618600-31619200	Enhancers	Adipose Nuclei	Adipose
28	chr6:31618600-31619200	Genic enhancers	Brain Hippocampus Middle	brain
29	chr6:31618600-31619200	Genic enhancers	Colonic Mucosa	Colon
30	chr6:31618600-31619200	Enhancers	Fetal Heart	heart
31	chr6:31618600-31619200	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
32	chr6:31618600-31619200	Genic enhancers	Fetal Intestine Small	intestine
33	chr6:31618600-31619200	Genic enhancers	Fetal Thymus	thymus
34	chr6:31618600-31619200	Genic enhancers	Rectal Mucosa Donor 29	rectum
35	chr6:31618600-31619200	Genic enhancers	Rectal Mucosa Donor 31	rectum
36	chr6:31618600-31619200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
37	chr6:31618600-31619200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
38	chr6:31618600-31619200	Genic enhancers	HSMMtube	muscle
39	chr6:31618600-31619400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:31618600-31619400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:31618600-31619400	Enhancers	Brain Cingulate Gyrus	brain
42	chr6:31618600-31619400	Flanking Active TSS	Brain Germinal Matrix	brain
43	chr6:31618600-31619400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:31618600-31619400	Enhancers	Small Intestine	intestine
45	chr6:31618600-31619400	Enhancers	Stomach Mucosa	stomach
46	chr6:31618600-31619400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
47	chr6:31618600-31619600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:31618600-31619600	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr6:31618600-31619800	Flanking Active TSS	Fetal Brain Male	brain
50	chr6:31618600-31619800	Transcr. at gene 5' and 3'	Dnd41	blood

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