Variant report

Variant	rs11609309
Chromosome Location	chr12:8171838-8171839
allele	G/T
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	JUND	chr12:8171523-8172076	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr12:8171087-8172099	H1-hESC	embryonic stem cell:	n/a	chr12:8171358-8171368 chr12:8171363-8171372
3	E2F6	chr12:8171170-8171953	H1-hESC	embryonic stem cell:	n/a	chr12:8171358-8171368 chr12:8171363-8171372
4	MAX	chr12:8171275-8171912	NB4	blood:	n/a	n/a
5	GATA1	chr12:8171154-8171838	PBDE	blood:	n/a	n/a
6	MAX	chr12:8171229-8171863	K562	blood:	n/a	n/a
7	SP1	chr12:8171435-8171980	H1-hESC	embryonic stem cell:	n/a	n/a
8	UBTF	chr12:8171455-8171923	K562	blood:	n/a	n/a
9	POLR2A	chr12:8171401-8171954	NB4	blood:	n/a	n/a
10	SIN3A	chr12:8171202-8172131	H1-hESC	embryonic stem cell:	n/a	chr12:8171367-8171378 chr12:8171748-8171759
11	EP300	chr12:8171432-8171951	H1-hESC	embryonic stem cell:	n/a	chr12:8171745-8171761 chr12:8171684-8171693
12	MYC	chr12:8171353-8172145	NB4	blood:	n/a	n/a
13	MAX	chr12:8171254-8172207	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTBP2	chr12:8171243-8172072	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr12:8171242-8171955	H1-hESC	embryonic stem cell:	n/a	n/a
16	TBP	chr12:8171539-8171841	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr12:8171181-8172230	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr12:8171720-8171870	GM12872	blood:	n/a	n/a
19	CREB1	chr12:8171260-8171899	H1-hESC	embryonic stem cell:	n/a	n/a
20	UBTF	chr12:8171359-8171946	K562	blood:	n/a	n/a
21	SP4	chr12:8171464-8171942	H1-hESC	embryonic stem cell:	n/a	n/a
22	CHD2	chr12:8171454-8172171	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:8171182..8172888-chr12:8173729..8176530,2	K562	blood:
2	chr12:8088481..8090137-chr12:8171670..8173575,2	K562	blood:

Variant related genes	Relation type
ENSG00000255581	TF binding region
ENSG00000059804	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10732571	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10846285	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10846331	0.98[ASN][1000 genomes]
rs10846333	0.98[ASN][1000 genomes]
rs10846366	0.82[ASN][1000 genomes]
rs11056779	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11056780	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11056782	0.89[EUR][1000 genomes]
rs11056783	0.89[EUR][1000 genomes]
rs11611693	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12811781	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12813762	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817051	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12818249	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818933	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819689	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12820720	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12820845	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823208	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12825574	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12831827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4301853	0.84[ASN][1000 genomes]
rs4310684	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4628755	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4883470	0.96[ASN][1000 genomes]
rs58279638	0.86[ASN][1000 genomes]
rs6488820	0.95[ASN][1000 genomes]
rs7137199	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7294894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299161	0.96[ASN][1000 genomes]
rs7299583	0.96[ASN][1000 genomes]
rs7313508	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7313772	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7958000	1.00[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7963223	0.98[ASN][1000 genomes]
rs7974225	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048545	chr12:7778760-8608231	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv541368	chr12:7778760-8608231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	esv1795892	chr12:7856819-8508693	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2758292	chr12:7856819-8623987	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	esv2759877	chr12:7856819-8623987	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv428270	chr12:7856819-8623987	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
7	nsv1054331	chr12:7924713-8183422	Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	esv1797934	chr12:7985460-8214261	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	esv1793572	chr12:7995827-8568422	Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
10	esv1792916	chr12:8000336-8171838	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv469082	chr12:8000336-8171838	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv469084	chr12:8000336-8171838	Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv469085	chr12:8000336-8171838	Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv469086	chr12:8000336-8171838	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
15	nsv557298	chr12:8000336-8171838	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised 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 target site	35 gene(s)	inside rSNPs	diseases
16	nsv541384	chr12:8003214-8188846	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
17	nsv1040972	chr12:8003413-8266291	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
18	nsv541388	chr12:8003413-8266291	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
19	nsv916941	chr12:8003501-8608220	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
20	esv2751118	chr12:8017473-8190206	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
21	nsv869752	chr12:8026388-8174912	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
22	nsv898729	chr12:8044997-8190206	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS 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 lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
23	nsv1045521	chr12:8123225-8242846	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
24	nsv898732	chr12:8123306-8190206	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
25	nsv1044509	chr12:8130958-8182060	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11609309	FOXJ2	cis	parietal	SCAN
rs11609309	CD163	cis	parietal	SCAN
rs11609309	CLEC4D	cis	parietal	SCAN
rs11609309	PRB4	cis	cerebellum	SCAN
rs11609309	CLEC2D	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8170800-8172000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr12:8170800-8172000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr12:8170800-8172200	Active TSS	H1 Cell Line	embryonic stem cell
4	chr12:8170800-8172200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:8170800-8172200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:8170800-8172200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:8170800-8172400	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr12:8171000-8172000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:8171000-8172000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:8171000-8172000	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr12:8171000-8172000	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr12:8171000-8172000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
13	chr12:8171000-8172000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:8171000-8172000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr12:8171000-8172000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:8171000-8172000	Bivalent/Poised TSS	Fetal Brain Female	brain
17	chr12:8171000-8172000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
18	chr12:8171000-8172200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr12:8171000-8172200	Active TSS	H9 Cell Line	embryonic stem cell
20	chr12:8171000-8172200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:8171000-8172200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr12:8171000-8172200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:8171000-8172200	Flanking Bivalent TSS/Enh	Dnd41	blood
24	chr12:8171200-8172000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr12:8171200-8172000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr12:8171200-8172000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
27	chr12:8171200-8172000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:8171200-8172000	Active TSS	Brain Angular Gyrus	brain
29	chr12:8171200-8172000	Active TSS	Brain Substantia Nigra	brain
30	chr12:8171200-8172000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
31	chr12:8171200-8172000	Bivalent/Poised TSS	A549	lung
32	chr12:8171200-8172200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:8171200-8172200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:8171200-8172200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:8171200-8172200	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr12:8171200-8172200	Active TSS	Brain Anterior Caudate	brain
37	chr12:8171200-8172200	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr12:8171200-8172200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
39	chr12:8171200-8172400	Active TSS	Thymus	Thymus
40	chr12:8171400-8172000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:8171400-8172000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
42	chr12:8171400-8172000	Bivalent Enhancer	Fetal Intestine Large	intestine
43	chr12:8171400-8172000	Active TSS	Ovary	ovary
44	chr12:8171400-8172000	Bivalent/Poised TSS	Psoas Muscle	Psoas
45	chr12:8171400-8172000	Bivalent Enhancer	Small Intestine	intestine
46	chr12:8171400-8172000	Bivalent Enhancer	GM12878-XiMat	blood
47	chr12:8171400-8172200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr12:8171600-8172000	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:8171600-8172000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
50	chr12:8171600-8172000	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach

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