Variant report

Variant	rs3794381
Chromosome Location	chr13:50073563-50073564
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:50070028..50071869-chr13:50072608..50075376,5	MCF-7	breast:
2	chr13:50072641..50077099-chr13:50079863..50082927,4	MCF-7	breast:
3	chr13:50016715..50020360-chr13:50068508..50074036,7	MCF-7	breast:
4	chr13:50071814..50073656-chr13:50077738..50079536,2	MCF-7	breast:
5	chr13:50072605..50075983-chr13:50085931..50088388,3	MCF-7	breast:
6	chr13:50061049..50067624-chr13:50068104..50073631,8	MCF-7	breast:
7	chr13:50068795..50071828-chr13:50072712..50075254,3	K562	blood:
8	chr13:50071845..50075663-chr13:50092471..50095842,3	K562	blood:
9	chr13:50068725..50070861-chr13:50073455..50076048,3	MCF-7	breast:
10	chr13:50068795..50071791-chr13:50072712..50074851,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000236577	Chromatin interaction
ENSG00000136147	Chromatin interaction
ENSG00000102547	Chromatin interaction
ENSG00000136169	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12050042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1409016	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1536194	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1555530	0.94[ASN][1000 genomes]
rs1812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1980794	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1980795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1998782	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2057415	0.92[ASN][1000 genomes]
rs2057417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2407689	0.90[ASN][1000 genomes]
rs3764085	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4468500	0.88[ASN][1000 genomes]
rs4941642	0.92[ASN][1000 genomes]
rs4942831	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4942832	0.89[ASN][1000 genomes]
rs71188363	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7139634	0.94[ASN][1000 genomes]
rs721458	0.90[ASN][1000 genomes]
rs7329078	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7338755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7987293	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7994115	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7994130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7998427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526569	0.90[JPT][hapmap]
rs9535248	0.90[ASN][1000 genomes]
rs9535249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9568219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9568223	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9591264	0.83[AFR][1000 genomes]
rs967163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs967164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3794381	PHF11	cis	Thyroid	GTEx
rs3794381	PHF11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 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	chr13:50070800-50073600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:50070800-50073600	Weak transcription	HMEC	breast
4	chr13:50070800-50074200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:50070800-50074400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr13:50070800-50074400	Weak transcription	Small Intestine	intestine
7	chr13:50070800-50074800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr13:50070800-50076200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:50070800-50076200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr13:50070800-50076400	Weak transcription	Fetal Lung	lung
11	chr13:50070800-50076800	Weak transcription	Left Ventricle	heart
12	chr13:50070800-50077000	Weak transcription	Gastric	stomach
13	chr13:50070800-50086600	Weak transcription	Psoas Muscle	Psoas
14	chr13:50070800-50086800	Weak transcription	Ovary	ovary
15	chr13:50070800-50087400	Weak transcription	Placenta	Placenta
16	chr13:50070800-50087600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr13:50070800-50087800	Weak transcription	Aorta	Aorta
18	chr13:50070800-50087800	Weak transcription	NHEK	skin
19	chr13:50070800-50088000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr13:50070800-50088000	Weak transcription	Brain Anterior Caudate	brain
21	chr13:50070800-50088000	Weak transcription	Esophagus	oesophagus
22	chr13:50070800-50088000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr13:50070800-50088200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr13:50070800-50088200	Weak transcription	Brain Substantia Nigra	brain
25	chr13:50070800-50095600	Weak transcription	Fetal Kidney	kidney
26	chr13:50071000-50073600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr13:50071000-50073600	Weak transcription	HSMM	muscle
28	chr13:50071000-50074200	Weak transcription	HSMMtube	muscle
29	chr13:50071000-50074400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr13:50071000-50074400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr13:50071000-50074800	Weak transcription	Fetal Stomach	stomach
32	chr13:50071000-50075000	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr13:50071000-50076600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr13:50071000-50076800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr13:50071000-50076800	Weak transcription	Adipose Nuclei	Adipose
36	chr13:50071000-50077000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr13:50071000-50077200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr13:50071000-50077800	Weak transcription	Fetal Intestine Small	intestine
39	chr13:50071000-50078200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr13:50071000-50079800	Weak transcription	Brain Hippocampus Middle	brain
41	chr13:50071000-50087800	Weak transcription	Colonic Mucosa	Colon
42	chr13:50071000-50087800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr13:50071000-50087800	Weak transcription	Right Ventricle	heart
44	chr13:50071000-50088000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr13:50071000-50093400	Weak transcription	HepG2	liver
46	chr13:50071200-50081600	Weak transcription	Thymus	Thymus
47	chr13:50071400-50075000	Strong transcription	Primary hematopoietic stem cells	blood
48	chr13:50071400-50075000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
49	chr13:50071400-50076800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr13:50071400-50081600	Weak transcription	Fetal Muscle Leg	muscle

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