Variant report

Variant	rs9568227
Chromosome Location	chr13:50079761-50079762
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs17381926	0.81[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs41284778	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56737298	0.88[ASN][1000 genomes]
rs59837207	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs66771344	0.84[ASN][1000 genomes]
rs67714799	0.88[ASN][1000 genomes]
rs7317398	1.00[ASN][1000 genomes]
rs73190705	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7331182	0.82[ASN][1000 genomes]
rs9562880	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9562881	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9562882	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9562884	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9562887	0.81[ASN][1000 genomes]
rs9562888	1.00[ASN][1000 genomes]
rs9568205	0.83[AMR][1000 genomes]
rs9568207	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9568209	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9568210	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9568211	0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9568214	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9568215	0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9568216	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9568222	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9568231	1.00[ASN][1000 genomes]
rs9568240	0.82[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap]

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	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv430561	chr13:49930643-50089844	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv430566	chr13:49945247-50089844	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430570	chr13:49961137-50089844	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv523648	chr13:50005444-50086266	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv561613	chr13:50013622-50086266	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers 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	17 gene(s)	inside rSNPs	diseases
7	nsv900070	chr13:50013622-50087142	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv561614	chr13:50042983-50086253	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv561615	chr13:50042983-50086266	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9568227	PHF11	cis	brain	BrainEAC

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50070200-50089200	Weak transcription	Fetal Brain Male	brain
2	chr13:50070800-50086600	Weak transcription	Psoas Muscle	Psoas
3	chr13:50070800-50086800	Weak transcription	Ovary	ovary
4	chr13:50070800-50087400	Weak transcription	Placenta	Placenta
5	chr13:50070800-50087600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr13:50070800-50087800	Weak transcription	Aorta	Aorta
7	chr13:50070800-50087800	Weak transcription	NHEK	skin
8	chr13:50070800-50088000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr13:50070800-50088000	Weak transcription	Brain Anterior Caudate	brain
10	chr13:50070800-50088000	Weak transcription	Esophagus	oesophagus
11	chr13:50070800-50088000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr13:50070800-50088200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:50070800-50088200	Weak transcription	Brain Substantia Nigra	brain
14	chr13:50070800-50095600	Weak transcription	Fetal Kidney	kidney
15	chr13:50071000-50079800	Weak transcription	Brain Hippocampus Middle	brain
16	chr13:50071000-50087800	Weak transcription	Colonic Mucosa	Colon
17	chr13:50071000-50087800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr13:50071000-50087800	Weak transcription	Right Ventricle	heart
19	chr13:50071000-50088000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr13:50071000-50093400	Weak transcription	HepG2	liver
21	chr13:50071200-50081600	Weak transcription	Thymus	Thymus
22	chr13:50071400-50081600	Weak transcription	Fetal Muscle Leg	muscle
23	chr13:50071400-50087000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr13:50071400-50087200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr13:50071800-50087200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr13:50071800-50088000	Weak transcription	Pancreas	Pancrea
27	chr13:50073800-50081600	Weak transcription	Liver	Liver
28	chr13:50074000-50093000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr13:50074600-50081400	Weak transcription	Dnd41	blood
30	chr13:50074800-50086400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr13:50075000-50080800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr13:50075000-50086800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr13:50075000-50087000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr13:50075000-50087800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr13:50075000-50087800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr13:50075000-50088200	Weak transcription	HMEC	breast
37	chr13:50075000-50102400	Weak transcription	NH-A	brain
38	chr13:50075000-50143800	Weak transcription	Small Intestine	intestine
39	chr13:50075200-50080200	Weak transcription	Fetal Stomach	stomach
40	chr13:50075200-50081400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr13:50075200-50087800	Weak transcription	Osteobl	bone
42	chr13:50075400-50088000	Weak transcription	Colon Smooth Muscle	Colon
43	chr13:50075600-50081200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr13:50077400-50080600	Weak transcription	Primary B cells from cord blood	blood
45	chr13:50077400-50083600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr13:50077400-50087800	Weak transcription	Left Ventricle	heart
47	chr13:50077600-50079800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr13:50077600-50080000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr13:50077600-50081600	Weak transcription	HUVEC	blood vessel
50	chr13:50077600-50086600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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