Variant report

Variant	rs12099427
Chromosome Location	chr11:47639153-47639154
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	CTCF	chr11:47639040-47639190	GM06990	blood:	n/a	n/a
2	CTCF	chr11:47638343-47639309	SK-N-SH	brain:	n/a	chr11:47638762-47638783 chr11:47638768-47638784 chr11:47638773-47638782 chr11:47638767-47638785
3	SMC3	chr11:47638380-47639488	SK-N-SH	brain:	n/a	chr11:47638769-47638783
4	MAFK	chr11:47638753-47639321	IMR90	lung:	n/a	n/a
5	RAD21	chr11:47638554-47639263	IMR90	lung:	n/a	chr11:47638765-47638784
6	RUNX3	chr11:47638955-47639338	GM12878	blood:	n/a	n/a
7	PML	chr11:47638462-47639376	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:47638442-47639234	PANC-1	pancreas:	n/a	n/a
9	RUNX3	chr11:47638970-47639388	GM12878	blood:	n/a	n/a
10	BATF	chr11:47638974-47639244	GM12878	blood:	n/a	n/a
11	EBF1	chr11:47638720-47639170	GM12878	blood:	n/a	chr11:47639052-47639063

No.	Distal block	Cell Line	Cell type
1	chr11:47636685..47639301-chr11:47641827..47644526,2	K562	blood:
2	chr11:47626940..47628624-chr11:47637270..47639878,2	MCF-7	breast:
3	chr11:47638979..47640654-chr11:47662400..47665038,2	K562	blood:
4	chr11:47395201..47395975-chr11:47638731..47639268,2	MCF-7	breast:
5	chr11:47556504..47558457-chr11:47638712..47641328,2	K562	blood:

Variant related genes	Relation type
ENSG00000223187	TF binding region
ENSG00000109919	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11039213	1.00[AMR][1000 genomes]
rs11039229	1.00[AMR][1000 genomes]
rs12099130	1.00[ASW][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2010519	1.00[AMR][1000 genomes]
rs2053978	1.00[AMR][1000 genomes]
rs2176403	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34037785	1.00[AMR][1000 genomes]
rs35976340	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56866638	1.00[AMR][1000 genomes]
rs56948110	1.00[AMR][1000 genomes]
rs57572703	1.00[AMR][1000 genomes]
rs60580032	1.00[AMR][1000 genomes]
rs7123107	1.00[AMR][1000 genomes]
rs7950077	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs896814	1.00[AMR][1000 genomes]
rs908597	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv825872	chr11:47565425-47660330	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47617600-47643200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr11:47618000-47639200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr11:47621000-47640400	Weak transcription	Fetal Brain Female	brain
4	chr11:47621600-47647600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:47621800-47642000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:47626400-47639200	Weak transcription	Colonic Mucosa	Colon
7	chr11:47627800-47643200	Weak transcription	Pancreas	Pancrea
8	chr11:47628800-47642000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:47629400-47639600	Weak transcription	HMEC	breast
10	chr11:47629800-47640800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:47629800-47642400	Weak transcription	Colon Smooth Muscle	Colon
12	chr11:47630000-47639800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr11:47630000-47641200	Weak transcription	Small Intestine	intestine
14	chr11:47630000-47642200	Weak transcription	Fetal Brain Male	brain
15	chr11:47630200-47639200	Weak transcription	Placenta	Placenta
16	chr11:47630200-47639600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr11:47630200-47640200	Weak transcription	HSMM	muscle
18	chr11:47630400-47648600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:47630400-47649600	Weak transcription	Fetal Heart	heart
20	chr11:47631000-47639200	Strong transcription	Fetal Intestine Small	intestine
21	chr11:47631200-47642400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr11:47631400-47639400	Weak transcription	HUVEC	blood vessel
23	chr11:47631400-47640600	Weak transcription	Brain Germinal Matrix	brain
24	chr11:47633000-47640600	Weak transcription	Aorta	Aorta
25	chr11:47633000-47641800	Weak transcription	Spleen	Spleen
26	chr11:47633200-47641400	Weak transcription	Gastric	stomach
27	chr11:47633200-47642000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr11:47633200-47642000	Weak transcription	Esophagus	oesophagus
29	chr11:47633600-47641400	Weak transcription	Psoas Muscle	Psoas
30	chr11:47633600-47647200	Weak transcription	Right Ventricle	heart
31	chr11:47633800-47640600	Weak transcription	Lung	lung
32	chr11:47633800-47641800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:47635000-47642400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr11:47635400-47642000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr11:47635400-47643200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr11:47635600-47639400	Weak transcription	Brain Substantia Nigra	brain
37	chr11:47635600-47640400	Weak transcription	NHEK	skin
38	chr11:47635800-47643200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr11:47636400-47642000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:47636600-47641800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr11:47636600-47661400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:47636800-47640600	Strong transcription	A549	lung
43	chr11:47636800-47653800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:47637000-47639200	Weak transcription	Fetal Lung	lung
45	chr11:47637000-47653400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr11:47637600-47639200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr11:47637600-47639200	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr11:47637600-47640200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr11:47637600-47648800	Strong transcription	Fetal Intestine Large	intestine
50	chr11:47637600-47650800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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