Variant report

Variant	rs12198593
Chromosome Location	chr6:2247049-2247050
allele	A/G
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	POLR2A	chr6:2245173-2247056	HepG2	liver:	n/a	n/a
2	JUN	chr6:2244606-2247054	K562	blood:	n/a	chr6:2246619-2246627 chr6:2246618-2246628 chr6:2246618-2246628 chr6:2246321-2246331 chr6:2246994-2247005 chr6:2246618-2246628 chr6:2246618-2246628
3	NFIC	chr6:2246253-2247064	ECC-1	luminal epithelium:	n/a	chr6:2246661-2246677 chr6:2246661-2246678
4	POLR2A	chr6:2245588-2247155	HepG2	liver:	n/a	n/a
5	SIN3AK20	chr6:2245958-2247054	MCF-7	breast:	n/a	n/a
6	MYBL2	chr6:2244975-2247172	HepG2	liver:	n/a	n/a
7	ZEB1	chr6:2244538-2247191	HepG2	liver:	n/a	chr6:2245548-2245557 chr6:2245548-2245560 chr6:2245266-2245278
8	POLR2A	chr6:2245632-2247075	GM12878	blood:	n/a	n/a
9	MBD4	chr6:2245903-2247074	HepG2	liver:	n/a	n/a
10	MYBL2	chr6:2245886-2247069	HepG2	liver:	n/a	n/a
11	SMARCC1	chr6:2245124-2247094	Hela-S3	cervix:	n/a	chr6:2246618-2246627
12	POLR2A	chr6:2245948-2247158	K562	blood:	n/a	n/a
13	POLR2A	chr6:2245261-2247063	GM19099	blood:	n/a	n/a
14	NFIC	chr6:2245609-2247129	HepG2	liver:	n/a	chr6:2246661-2246677 chr6:2246661-2246678
15	NFIC	chr6:2245881-2247110	HepG2	liver:	n/a	chr6:2246661-2246677 chr6:2246661-2246678

No.	Distal block	Cell Line	Cell type
1	chr6:2244284..2246271-chr6:2246300..2249565,3	K562	blood:
2	chr6:1608353..1611335-chr6:2245492..2248463,2	MCF-7	breast:
3	chr6:2245961..2247714-chr7:148785779..148788707,2	MCF-7	breast:

Variant related genes	Relation type
GMDS	TF binding region
ENSG00000054598	Chromatin interaction
ENSG00000250903	Chromatin interaction
ENSG00000197362	Chromatin interaction
ENSG00000112699	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10458134	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11242746	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11242747	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11242751	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11242753	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11242755	0.84[AMR][1000 genomes]
rs11242756	0.82[AMR][1000 genomes]
rs12189724	1.00[YRI][hapmap]
rs12198715	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12207377	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12209836	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12215421	0.84[AMR][1000 genomes]
rs12215717	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12216224	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12523924	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12525444	0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12529507	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs12529715	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12660715	0.82[AMR][1000 genomes]
rs12664420	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12665003	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12665493	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13194365	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13195362	0.87[AMR][1000 genomes]
rs13196348	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13196472	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13202573	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13206299	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13215846	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17134819	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2129178	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2295009	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34244401	0.84[AMR][1000 genomes]
rs34439821	0.84[AMR][1000 genomes]
rs35063859	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35410074	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3800189	0.90[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3817904	1.00[YRI][hapmap]
rs3929752	0.84[AMR][1000 genomes]
rs58348518	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60015886	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73342732	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7452388	0.82[AMR][1000 genomes]
rs9501817	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9647650	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv1025814	chr6:2064629-2308518	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538098	chr6:2064629-2308518	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv1030181	chr6:2071210-2308657	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv538099	chr6:2071210-2308657	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
8	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
9	nsv830573	chr6:2120985-2263646	Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv1022623	chr6:2199666-2267750	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv538100	chr6:2199666-2267750	ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv1022166	chr6:2199666-2320800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
13	nsv1017174	chr6:2213893-2340529	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
14	nsv1033201	chr6:2218647-2308518	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
15	nsv538101	chr6:2218647-2308518	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
16	nsv1026678	chr6:2230064-2261297	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	n/a
17	esv2763526	chr6:2230064-2311916	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
18	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
19	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2244600-2247200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:2244600-2247200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr6:2245200-2247200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:2246000-2247200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:2246200-2247200	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr6:2246200-2247200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:2246400-2247200	Flanking Active TSS	Dnd41	blood
8	chr6:2246600-2247200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:2246600-2247200	Flanking Active TSS	Liver	Liver
10	chr6:2246600-2247200	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr6:2246600-2247200	Flanking Active TSS	Fetal Intestine Small	intestine
12	chr6:2246600-2247200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr6:2246600-2247200	Flanking Active TSS	Hela-S3	cervix
14	chr6:2246600-2247200	Flanking Active TSS	HepG2	liver
15	chr6:2246600-2248600	Enhancers	Small Intestine	intestine
16	chr6:2246800-2247200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:2246800-2247200	Enhancers	Fetal Lung	lung
18	chr6:2246800-2247200	Enhancers	Placenta	Placenta
19	chr6:2246800-2247200	Enhancers	Placenta Amnion	Placenta Amnion
20	chr6:2246800-2247200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
21	chr6:2246800-2247200	Flanking Active TSS	GM12878-XiMat	blood
22	chr6:2246800-2247800	Enhancers	Primary B cells from peripheral blood	blood
23	chr6:2246800-2248200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr6:2246800-2248200	Enhancers	Primary T cells fromperipheralblood	blood
25	chr6:2246800-2248600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr6:2246800-2248600	Enhancers	Fetal Thymus	thymus
27	chr6:2246800-2249000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:2246800-2249000	Weak transcription	Ovary	ovary
29	chr6:2246800-2250000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:2246800-2250800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:2246800-2254800	Weak transcription	Esophagus	oesophagus
32	chr6:2246800-2255800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:2246800-2264200	Weak transcription	Gastric	stomach
34	chr6:2247000-2247200	Enhancers	H1 Cell Line	embryonic stem cell
35	chr6:2247000-2247200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:2247000-2247200	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr6:2247000-2247200	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr6:2247000-2247200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:2247000-2247200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:2247000-2247200	Enhancers	Primary B cells from cord blood	blood
41	chr6:2247000-2247200	Active TSS	Primary hematopoietic stem cells	blood
42	chr6:2247000-2247200	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr6:2247000-2247200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:2247000-2247200	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr6:2247000-2247200	Enhancers	Adipose Nuclei	Adipose
46	chr6:2247000-2247200	Enhancers	Brain Anterior Caudate	brain
47	chr6:2247000-2247200	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr6:2247000-2247200	Enhancers	Colon Smooth Muscle	Colon
49	chr6:2247000-2247200	Enhancers	Fetal Muscle Leg	muscle
50	chr6:2247000-2247200	Active TSS	Rectal Smooth Muscle	rectum

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