Variant report

Variant	rs529948
Chromosome Location	chr6:44236369-44236370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr6:44235547-44236523	SK-N-SH	brain:	n/a	chr6:44235925-44235944 chr6:44235778-44235790
2	SIN3A	chr6:44235722-44236699	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chr6:44235890-44236650	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr6:44235563-44236375	HCT-116	colon:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
5	POLR2A	chr6:44235731-44236547	H1-neurons	neurons:	n/a	n/a
6	CTCF	chr6:44236260-44236410	WI-38	lung:	n/a	n/a
7	POLR2A	chr6:44235768-44236525	H1-neurons	neurons:	n/a	n/a
8	REST	chr6:44235753-44236832	H1-neurons	neurons:	n/a	n/a
9	CTCF	chr6:44235549-44236536	SK-N-SH	brain:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
10	SMC3	chr6:44235580-44236925	SK-N-SH	brain:	n/a	n/a
11	RAD21	chr6:44235564-44236390	HCT-116	colon:	n/a	chr6:44235925-44235944 chr6:44235778-44235790

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:44235432..44236394-chr6:44272155..44273117,4	MCF-7	breast:
2	chr6:43857455..43859614-chr6:44235657..44237353,2	K562	blood:
3	chr6:44235250..44236905-chr6:44304916..44306810,16	MCF-7	breast:
4	chr6:44235516..44236382-chr6:44423771..44424641,3	K562	blood:
5	chr6:44234643..44237474-chr6:44296098..44297940,2	MCF-7	breast:
6	chr6:44233082..44237547-chr6:44353791..44357282,5	MCF-7	breast:
7	chr6:44234588..44237594-chr6:44277478..44280850,3	MCF-7	breast:
8	chr6:44235750..44236849-chr6:44272248..44273140,3	MCF-7	breast:
9	chr6:44084290..44087287-chr6:44233720..44236514,2	K562	blood:
10	chr6:44064118..44064933-chr6:44235897..44236470,2	K562	blood:
11	chr6:44235926..44236686-chr6:44263668..44264282,2	K562	blood:
12	chr6:44235852..44236696-chr6:44437202..44438131,2	MCF-7	breast:
13	chr6:44235214..44237013-chr6:44305028..44307078,2	MCF-7	breast:
14	chr6:44235278..44236426-chr6:44305941..44306986,11	K562	blood:
15	chr6:44235532..44236481-chr6:44305932..44306869,8	MCF-7	breast:

No data

Variant related genes	Relation type
NFKBIE	TF binding region
TMEM151B	TF binding region
ENSG00000272442	TF binding region
ENSG00000096401	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10807297	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs1123523	0.86[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12205227	0.82[ASN][1000 genomes]
rs12215176	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12664825	0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12943	0.88[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs170510	0.94[ASN][1000 genomes]
rs2297335	0.83[ASN][1000 genomes]
rs2297336	0.86[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs324138	0.84[ASN][1000 genomes]
rs324139	0.88[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs324140	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs324142	0.83[ASN][1000 genomes]
rs324144	0.83[ASN][1000 genomes]
rs324145	0.86[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs324146	0.86[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs324147	0.83[ASN][1000 genomes]
rs325017	0.84[ASN][1000 genomes]
rs325018	0.84[ASN][1000 genomes]
rs325019	0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs3734710	0.95[ASN][1000 genomes]
rs4714773	0.95[ASN][1000 genomes]
rs4714774	0.84[ASN][1000 genomes]
rs516582	0.88[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs524533	0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs545970	0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs551145	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs557373	0.83[ASN][1000 genomes]
rs570469	0.84[ASN][1000 genomes]
rs571770	0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs614715	0.83[ASN][1000 genomes]
rs694349	0.84[ASN][1000 genomes]
rs844315	0.87[ASN][1000 genomes]
rs9369469	0.84[ASN][1000 genomes]
rs9381305	0.84[ASN][1000 genomes]
rs9381306	0.84[ASN][1000 genomes]
rs9381307	0.86[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9381308	0.86[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9395000	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9395001	0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv885851	chr6:44178471-44240559	Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
3	nsv603003	chr6:44191920-44253765	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv524398	chr6:44200953-44253765	Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
10	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
11	nsv885857	chr6:44223010-44250165	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 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	chr6:44233400-44237000	Weak transcription	HMEC	breast
2	chr6:44233400-44237200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:44233400-44237400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:44233400-44237800	Weak transcription	Pancreas	Pancrea
5	chr6:44233400-44237800	Weak transcription	Right Ventricle	heart
6	chr6:44233600-44238000	Weak transcription	Right Atrium	heart
7	chr6:44234600-44237200	Weak transcription	Spleen	Spleen
8	chr6:44234800-44238000	Enhancers	GM12878-XiMat	blood
9	chr6:44235400-44237800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr6:44235600-44236400	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr6:44235600-44236400	Bivalent Enhancer	HepG2	liver
12	chr6:44235800-44236400	Enhancers	Brain Hippocampus Middle	brain
13	chr6:44235800-44236400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr6:44235800-44236400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:44235800-44236600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:44235800-44236600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:44235800-44236600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr6:44235800-44237600	Enhancers	Brain Germinal Matrix	brain
19	chr6:44236000-44236400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
20	chr6:44236000-44236400	Enhancers	Fetal Heart	heart
21	chr6:44236000-44236400	Bivalent Enhancer	Fetal Stomach	stomach
22	chr6:44236000-44236600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr6:44236000-44236600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:44236000-44236600	Bivalent Enhancer	Fetal Thymus	thymus
25	chr6:44236000-44236800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
26	chr6:44236000-44236800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:44236000-44236800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr6:44236000-44236800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:44236000-44237000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:44236000-44237000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:44236000-44237200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr6:44236000-44237600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:44236000-44237600	Enhancers	Fetal Brain Male	brain
34	chr6:44236000-44237600	Enhancers	Fetal Brain Female	brain
35	chr6:44236200-44236400	Active TSS	H9 Cell Line	embryonic stem cell
36	chr6:44236200-44236400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
37	chr6:44236200-44236400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr6:44236200-44236400	Enhancers	Brain Substantia Nigra	brain
39	chr6:44236200-44236600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:44236200-44236600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
41	chr6:44236200-44236800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:44236200-44236800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
43	chr6:44236200-44237200	Weak transcription	Brain Anterior Caudate	brain
44	chr6:44236200-44237800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:44236200-44238400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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