Variant report

Variant	rs6561528
Chromosome Location	chr13:50074752-50074753
allele	A/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 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	chr13:50072605..50075983-chr13:50085931..50088388,3	MCF-7	breast:
4	chr13:50068795..50071828-chr13:50072712..50075254,3	K562	blood:
5	chr13:50033311..50035354-chr13:50074002..50076664,2	MCF-7	breast:
6	chr13:50071845..50075663-chr13:50092471..50095842,3	K562	blood:
7	chr13:50068725..50070861-chr13:50073455..50076048,3	MCF-7	breast:
8	chr13:50068795..50071791-chr13:50072712..50074851,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000136147	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1543514	0.87[ASN][1000 genomes]
rs2031532	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2057413	0.91[ASN][1000 genomes]
rs2147985	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2407692	0.87[ASN][1000 genomes]
rs2407693	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4142285	0.91[ASN][1000 genomes]
rs4417458	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4942835	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6561525	0.91[ASN][1000 genomes]
rs6561527	0.95[ASN][1000 genomes]
rs6561529	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561531	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7319587	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7321228	0.91[ASN][1000 genomes]
rs7324622	0.95[ASN][1000 genomes]
rs7328782	0.91[ASN][1000 genomes]
rs7337488	0.95[ASN][1000 genomes]
rs7982297	0.87[ASN][1000 genomes]
rs7992603	0.87[ASN][1000 genomes]
rs7996852	0.91[ASN][1000 genomes]
rs8000149	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526564	0.91[ASN][1000 genomes]
rs959421	0.94[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6561528	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	chr13:50070800-50074800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr13:50070800-50076200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:50070800-50076200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr13:50070800-50076400	Weak transcription	Fetal Lung	lung
6	chr13:50070800-50076800	Weak transcription	Left Ventricle	heart
7	chr13:50070800-50077000	Weak transcription	Gastric	stomach
8	chr13:50070800-50086600	Weak transcription	Psoas Muscle	Psoas
9	chr13:50070800-50086800	Weak transcription	Ovary	ovary
10	chr13:50070800-50087400	Weak transcription	Placenta	Placenta
11	chr13:50070800-50087600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr13:50070800-50087800	Weak transcription	Aorta	Aorta
13	chr13:50070800-50087800	Weak transcription	NHEK	skin
14	chr13:50070800-50088000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr13:50070800-50088000	Weak transcription	Brain Anterior Caudate	brain
16	chr13:50070800-50088000	Weak transcription	Esophagus	oesophagus
17	chr13:50070800-50088000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr13:50070800-50088200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr13:50070800-50088200	Weak transcription	Brain Substantia Nigra	brain
20	chr13:50070800-50095600	Weak transcription	Fetal Kidney	kidney
21	chr13:50071000-50074800	Weak transcription	Fetal Stomach	stomach
22	chr13:50071000-50075000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr13:50071000-50076600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr13:50071000-50076800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr13:50071000-50076800	Weak transcription	Adipose Nuclei	Adipose
26	chr13:50071000-50077000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr13:50071000-50077200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr13:50071000-50077800	Weak transcription	Fetal Intestine Small	intestine
29	chr13:50071000-50078200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr13:50071000-50079800	Weak transcription	Brain Hippocampus Middle	brain
31	chr13:50071000-50087800	Weak transcription	Colonic Mucosa	Colon
32	chr13:50071000-50087800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr13:50071000-50087800	Weak transcription	Right Ventricle	heart
34	chr13:50071000-50088000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr13:50071000-50093400	Weak transcription	HepG2	liver
36	chr13:50071200-50081600	Weak transcription	Thymus	Thymus
37	chr13:50071400-50075000	Strong transcription	Primary hematopoietic stem cells	blood
38	chr13:50071400-50075000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
39	chr13:50071400-50076800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr13:50071400-50081600	Weak transcription	Fetal Muscle Leg	muscle
41	chr13:50071400-50087000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr13:50071400-50087200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr13:50071600-50075000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr13:50071600-50075200	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr13:50071600-50078400	Strong transcription	Fetal Thymus	thymus
46	chr13:50071800-50087200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr13:50071800-50088000	Weak transcription	Pancreas	Pancrea
48	chr13:50072000-50075000	Strong transcription	Primary B cells from cord blood	blood
49	chr13:50072000-50075000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr13:50072000-50078400	Strong transcription	Monocytes-CD14+_RO01746	blood

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