Variant report

Variant	rs11628131
Chromosome Location	chr14:36994609-36994610
allele	A/C
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	RAD21	chr14:36993936-36995125	H1-hESC	embryonic stem cell:	n/a	chr14:36994150-36994162 chr14:36994027-36994034 chr14:36994148-36994167 chr14:36994886-36994898 chr14:36994884-36994903 chr14:36994151-36994164
2	CTCF	chr14:36994606-36995132	K562	blood:	n/a	chr14:36994881-36994902 chr14:36994886-36994904 chr14:36994888-36994901 chr14:36994887-36994903
3	CTCF	chr14:36994077-36994621	A549	lung:	n/a	chr14:36994152-36994165 chr14:36994152-36994165 chr14:36994150-36994168 chr14:36994151-36994167
4	CTCF	chr14:36993966-36995204	SK-N-SH	brain:	n/a	chr14:36994881-36994902 chr14:36994886-36994904 chr14:36994152-36994165 chr14:36994152-36994165 chr14:36994150-36994168 chr14:36994151-36994167 chr14:36994888-36994901 chr14:36994887-36994903
5	JUND	chr14:36994149-36995115	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr14:36993839-36995370	A549	lung:	n/a	chr14:36994881-36994902 chr14:36994886-36994904 chr14:36994152-36994165 chr14:36994152-36994165 chr14:36994150-36994168 chr14:36994151-36994167 chr14:36994888-36994901 chr14:36994887-36994903
7	RAD21	chr14:36993996-36995163	H1-hESC	embryonic stem cell:	n/a	chr14:36994150-36994162 chr14:36994027-36994034 chr14:36994148-36994167 chr14:36994886-36994898 chr14:36994884-36994903 chr14:36994151-36994164
8	CTCF	chr14:36993873-36995108	HepG2	liver:	n/a	chr14:36994881-36994902 chr14:36994886-36994904 chr14:36994152-36994165 chr14:36994152-36994165 chr14:36994150-36994168 chr14:36994151-36994167 chr14:36994888-36994901 chr14:36994887-36994903
9	SUZ12	chr14:36990826-36995085	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr14:36994081-36995137	HCT-116	colon:	n/a	chr14:36994881-36994902 chr14:36994886-36994904 chr14:36994152-36994165 chr14:36994152-36994165 chr14:36994150-36994168 chr14:36994151-36994167 chr14:36994888-36994901 chr14:36994887-36994903
11	RAD21	chr14:36994533-36995178	HCT-116	colon:	n/a	chr14:36994886-36994898 chr14:36994884-36994903
12	RAD21	chr14:36994564-36995101	HepG2	liver:	n/a	chr14:36994886-36994898 chr14:36994884-36994903
13	BACH1	chr14:36994246-36994897	H1-hESC	embryonic stem cell:	n/a	n/a
14	SMC3	chr14:36994599-36995043	K562	blood:	n/a	chr14:36994888-36994902
15	CTCF	chr14:36993999-36995110	H1-hESC	embryonic stem cell:	n/a	chr14:36994881-36994902 chr14:36994886-36994904 chr14:36994152-36994165 chr14:36994152-36994165 chr14:36994150-36994168 chr14:36994151-36994167 chr14:36994888-36994901 chr14:36994887-36994903
16	CTCF	chr14:36994528-36995226	MCF-7	breast:	n/a	chr14:36994881-36994902 chr14:36994886-36994904 chr14:36994888-36994901 chr14:36994887-36994903
17	CTCF	chr14:36994480-36994630	HRPEpiC	eye:	n/a	n/a
18	CTCF	chr14:36993942-36995159	H1-hESC	embryonic stem cell:	n/a	chr14:36994881-36994902 chr14:36994886-36994904 chr14:36994152-36994165 chr14:36994152-36994165 chr14:36994150-36994168 chr14:36994151-36994167 chr14:36994888-36994901 chr14:36994887-36994903
19	CTCF	chr14:36994045-36995263	HCT-116	colon:	n/a	chr14:36994881-36994902 chr14:36994886-36994904 chr14:36994152-36994165 chr14:36994152-36994165 chr14:36994150-36994168 chr14:36994151-36994167 chr14:36994888-36994901 chr14:36994887-36994903
20	CTBP2	chr14:36993358-36995031	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:36994601..36995313-chr3:64253518..64254229,2	MCF-7	breast:
2	chr14:36574395..36574937-chr14:36994454..36995363,2	MCF-7	breast:
3	chr14:36676641..36677323-chr14:36994485..36995249,2	MCF-7	breast:
4	chr14:36877517..36878211-chr14:36994385..36995299,2	MCF-7	breast:
5	chr14:36986593..36988111-chr14:36992508..36994903,2	MCF-7	breast:
6	chr14:36918821..36920421-chr14:36994175..36995365,7	MCF-7	breast:

Variant related genes	Relation type
NKX2-1	TF binding region
ENSG00000163637	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10047867	0.85[EUR][1000 genomes]
rs10047954	0.88[EUR][1000 genomes]
rs10129663	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10139411	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10145174	0.90[EUR][1000 genomes]
rs10148530	0.90[EUR][1000 genomes]
rs10150267	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10483473	0.90[EUR][1000 genomes]
rs1076810	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11624944	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11625806	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11628208	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12884641	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17104686	0.90[EUR][1000 genomes]
rs1951165	0.86[EUR][1000 genomes]
rs1951166	0.86[EUR][1000 genomes]
rs1951167	0.84[ASW][hapmap]
rs35770599	0.86[EUR][1000 genomes]
rs4899401	0.84[ASW][hapmap];0.82[MKK][hapmap]
rs4903224	0.84[EUR][1000 genomes]
rs67268304	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7159131	0.86[EUR][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	nsv1040256	chr14:36501452-37172046	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv542040	chr14:36501452-37172046	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv1047290	chr14:36564568-37445157	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	nsv1037952	chr14:36670484-37294692	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv542042	chr14:36670484-37294692	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv1053685	chr14:36915643-37245920	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv917279	chr14:36953511-37146655	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11628131	SNX6	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:36991600-36995000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr14:36993400-36994800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr14:36993400-36995200	Bivalent Enhancer	Liver	Liver
4	chr14:36993600-36994800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr14:36993600-36995000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr14:36993600-36995000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr14:36993800-36994800	Bivalent Enhancer	Colonic Mucosa	Colon
8	chr14:36993800-36994800	Bivalent Enhancer	Right Ventricle	heart
9	chr14:36993800-36995000	Enhancers	Pancreas	Pancrea
10	chr14:36994000-36995200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr14:36994000-36995400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
12	chr14:36994000-36995400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
13	chr14:36994200-36994800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
14	chr14:36994200-36994800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:36994200-36994800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
16	chr14:36994200-36994800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr14:36994200-36994800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr14:36994200-36994800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
19	chr14:36994200-36994800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr14:36994200-36994800	Bivalent Enhancer	HMEC	breast
21	chr14:36994200-36995000	Bivalent Enhancer	Placenta	Placenta
22	chr14:36994200-36995000	Flanking Bivalent TSS/Enh	HepG2	liver
23	chr14:36994200-36995000	Bivalent/Poised TSS	NHEK	skin
24	chr14:36994200-36995200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr14:36994200-36995200	Bivalent Enhancer	Brain Hippocampus Middle	brain
26	chr14:36994200-36995200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
27	chr14:36994200-36995200	Bivalent/Poised TSS	A549	lung
28	chr14:36994400-36994800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
29	chr14:36994400-36994800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
30	chr14:36994400-36994800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr14:36994400-36994800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr14:36994400-36994800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
33	chr14:36994400-36994800	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
34	chr14:36994400-36995000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
35	chr14:36994400-36995200	Bivalent Enhancer	Adipose Nuclei	Adipose
36	chr14:36994600-36994800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr14:36994600-36994800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
38	chr14:36994600-36994800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
39	chr14:36994600-36994800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
40	chr14:36994600-36994800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
41	chr14:36994600-36994800	Bivalent Enhancer	Brain Angular Gyrus	brain
42	chr14:36994600-36994800	Bivalent Enhancer	Brain Anterior Caudate	brain
43	chr14:36994600-36994800	Bivalent Enhancer	Esophagus	oesophagus
44	chr14:36994600-36995000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell

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