Variant report

Variant	rs11791671
Chromosome Location	chr9:3398679-3398680
allele	C/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	NFIC	chr9:3397997-3398730	GM12878	blood:	n/a	n/a
2	YY1	chr9:3398351-3398734	GM12892	blood:	n/a	chr9:3398523-3398545 chr9:3398534-3398542
3	ZNF384	chr9:3397913-3398995	GM12878	blood:	n/a	n/a
4	POLR2A	chr9:3398257-3398773	GM12892	blood:	n/a	n/a
5	ATF2	chr9:3398074-3398747	GM12878	blood:	n/a	n/a
6	BCLAF1	chr9:3397900-3398826	GM12878	blood:	n/a	n/a
7	RCOR1	chr9:3397605-3398744	GM12878	blood:	n/a	n/a
8	SMC3	chr9:3398190-3398691	GM12878	blood:	n/a	chr9:3398542-3398549
9	NFIC	chr9:3397829-3398860	GM12878	blood:	n/a	n/a
10	SPI1	chr9:3397666-3398752	HL-60	blood:	n/a	chr9:3398309-3398316 chr9:3398307-3398320 chr9:3398301-3398314 chr9:3398307-3398320
11	CREB1	chr9:3397924-3398879	GM12878	blood:	n/a	n/a
12	YY1	chr9:3398225-3398767	GM12878	blood:	n/a	chr9:3398523-3398545 chr9:3398534-3398542
13	SPI1	chr9:3397686-3398708	GM12878	blood:	n/a	chr9:3398309-3398316 chr9:3398307-3398320 chr9:3398301-3398314 chr9:3398307-3398320
14	YY1	chr9:3398342-3398745	K562	blood:	n/a	chr9:3398523-3398545 chr9:3398534-3398542

Variant related genes	Relation type
RFX3	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11795111	0.89[CEU][hapmap]
rs13296217	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13298470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13300778	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34601938	1.00[AFR][1000 genomes]
rs34621673	1.00[AFR][1000 genomes]
rs34651968	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs34804475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36019927	1.00[AFR][1000 genomes]
rs36062993	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv613147	chr9:3368111-3440355	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv1849738	chr9:3389223-3404434	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
12	nsv892090	chr9:3391364-3496660	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3351000-3408200	Weak transcription	Fetal Intestine Small	intestine
2	chr9:3377600-3401400	Weak transcription	HMEC	breast
3	chr9:3377800-3401600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:3382200-3425000	Weak transcription	Aorta	Aorta
5	chr9:3382400-3401400	Weak transcription	Brain Anterior Caudate	brain
6	chr9:3382800-3401000	Weak transcription	Brain Germinal Matrix	brain
7	chr9:3383200-3410000	Weak transcription	Fetal Brain Male	brain
8	chr9:3383400-3401400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:3386200-3409600	Weak transcription	Psoas Muscle	Psoas
10	chr9:3387200-3401000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr9:3387200-3433800	Weak transcription	Pancreas	Pancrea
12	chr9:3387800-3401400	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:3388000-3401400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr9:3388200-3401400	Weak transcription	Brain Substantia Nigra	brain
15	chr9:3388600-3401800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:3388800-3401800	Weak transcription	Fetal Stomach	stomach
17	chr9:3390800-3401200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:3390800-3401600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:3391000-3401800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr9:3391800-3401200	Weak transcription	Brain Angular Gyrus	brain
21	chr9:3392200-3398800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:3392400-3401200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr9:3393600-3401400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr9:3395000-3401000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr9:3395600-3400800	Weak transcription	Fetal Brain Female	brain
26	chr9:3395800-3401400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:3396000-3401000	Weak transcription	Fetal Lung	lung
28	chr9:3396800-3401400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:3397000-3398800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr9:3397600-3398800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr9:3397600-3398800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr9:3397600-3398800	Flanking Active TSS	GM12878-XiMat	blood
33	chr9:3397800-3398800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr9:3397800-3398800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr9:3397800-3398800	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr9:3397800-3398800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr9:3397800-3398800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr9:3398000-3398800	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr9:3398000-3398800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr9:3398000-3398800	Enhancers	Fetal Kidney	kidney
41	chr9:3398000-3401200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr9:3398200-3398800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr9:3398200-3398800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr9:3398200-3401400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr9:3398200-3401600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr9:3398400-3398800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr9:3398400-3398800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr9:3398400-3398800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr9:3398400-3398800	Flanking Active TSS	Dnd41	blood
50	chr9:3398400-3399200	Enhancers	Small Intestine	intestine

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