Variant report

Variant	rs56325960
Chromosome Location	chr1:78342987-78342988
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17100791	0.87[EUR][1000 genomes]
rs17100850	1.00[EUR][1000 genomes]
rs17101048	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17101052	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17101082	0.84[ASN][1000 genomes]
rs17101109	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2296455	0.84[ASN][1000 genomes]
rs28362659	1.00[EUR][1000 genomes]
rs28362660	0.93[EUR][1000 genomes]
rs34128192	1.00[EUR][1000 genomes]
rs3767026	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3767027	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59087988	0.86[ASN][1000 genomes]
rs72685317	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1004327	chr1:78212804-78352385	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1006600	chr1:78222312-78384009	Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv535011	chr1:78222312-78384009	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78282800-78353400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr1:78298600-78352400	Weak transcription	Right Ventricle	heart
3	chr1:78299600-78343000	Weak transcription	K562	blood
4	chr1:78299600-78353800	Weak transcription	Brain Substantia Nigra	brain
5	chr1:78301400-78353200	Weak transcription	HSMMtube	muscle
6	chr1:78309200-78352400	Weak transcription	Aorta	Aorta
7	chr1:78312000-78353000	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:78313000-78353200	Weak transcription	HUVEC	blood vessel
9	chr1:78313400-78343200	Weak transcription	Pancreas	Pancrea
10	chr1:78324600-78353800	Weak transcription	Esophagus	oesophagus
11	chr1:78327200-78353600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:78327400-78353800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:78329600-78344400	Weak transcription	GM12878-XiMat	blood
14	chr1:78330000-78344400	Weak transcription	Small Intestine	intestine
15	chr1:78330800-78346600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:78333200-78343800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:78333400-78353000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:78333400-78353800	Weak transcription	Lung	lung
19	chr1:78333600-78346400	Weak transcription	Brain Anterior Caudate	brain
20	chr1:78333600-78352200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:78333600-78354000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:78333800-78352600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:78333800-78353800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:78334400-78343600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:78334400-78343800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:78334400-78345000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:78334400-78346200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:78334400-78346600	Weak transcription	Thymus	Thymus
29	chr1:78334400-78348400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:78334400-78350600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:78334400-78352600	Weak transcription	Left Ventricle	heart
32	chr1:78334400-78352600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:78334400-78353000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr1:78334400-78353200	Weak transcription	Fetal Lung	lung
35	chr1:78334400-78353600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:78334400-78353600	Weak transcription	Adipose Nuclei	Adipose
37	chr1:78334400-78353800	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:78334400-78353800	Weak transcription	Fetal Kidney	kidney
39	chr1:78334600-78345000	Weak transcription	Primary B cells from cord blood	blood
40	chr1:78334600-78345000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:78334600-78346200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:78334600-78346600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:78334600-78347200	Weak transcription	Fetal Thymus	thymus
44	chr1:78334600-78348800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:78334600-78352600	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:78334600-78353000	Weak transcription	Primary B cells from peripheral blood	blood
47	chr1:78334600-78353200	Weak transcription	HSMM	muscle
48	chr1:78334600-78353200	Weak transcription	Osteobl	bone
49	chr1:78334600-78353600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:78334600-78353600	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links