Variant report

Variant	rs59734390
Chromosome Location	chr1:224547807-224547808
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224545456..224548563-chr1:224564069..224566245,3	K562	blood:
2	chr1:224544599..224546252-chr1:224546494..224549421,2	MCF-7	breast:
3	chr1:224547136..224549294-chr1:224550559..224553232,2	K562	blood:
4	chr1:224544325..224548164-chr1:224620481..224623704,4	K562	blood:

Variant related genes	Relation type
ENSG00000143786	Chromatin interaction
ENSG00000162923	Chromatin interaction
ENSG00000143771	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10495218	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10495221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11800357	0.86[AMR][1000 genomes]
rs11804538	0.86[AMR][1000 genomes]
rs11807149	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11809688	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11809710	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11810160	1.00[AMR][1000 genomes]
rs11812007	1.00[AMR][1000 genomes]
rs16847675	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16847784	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16847858	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16847870	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16847871	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1857042	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2211327	0.86[AMR][1000 genomes]
rs57102803	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs57719044	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs58304668	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58649883	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs59577766	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs60063902	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60349703	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60627429	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs61000820	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs61278437	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs61590597	0.86[AMR][1000 genomes]
rs6674133	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6681611	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6702649	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs73121865	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs73123788	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs73123791	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs73125526	1.00[AMR][1000 genomes]
rs73125529	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs73125533	0.91[AFR][1000 genomes]
rs73125540	0.86[AMR][1000 genomes]
rs73125543	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224545200-224555200	Weak transcription	Spleen	Spleen
2	chr1:224545400-224553800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:224545400-224559000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:224545600-224555200	Weak transcription	Lung	lung
5	chr1:224545600-224555200	Weak transcription	Ovary	ovary
6	chr1:224545800-224549800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:224545800-224555000	Weak transcription	Brain Anterior Caudate	brain
8	chr1:224545800-224562800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:224545800-224605000	Weak transcription	Aorta	Aorta
10	chr1:224546000-224548000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr1:224546000-224548000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr1:224546000-224548400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:224546000-224548600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:224546000-224548600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:224546000-224548600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr1:224546000-224549800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:224546000-224551600	Weak transcription	Thymus	Thymus
18	chr1:224546000-224554600	Weak transcription	Liver	Liver
19	chr1:224546000-224555200	Weak transcription	Fetal Kidney	kidney
20	chr1:224546000-224556400	Weak transcription	Brain Angular Gyrus	brain
21	chr1:224546000-224563800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:224546000-224564400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:224546200-224548000	Enhancers	Fetal Brain Male	brain
24	chr1:224546200-224548000	Enhancers	HepG2	liver
25	chr1:224546200-224548600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:224546200-224548600	Enhancers	Primary T cells from cord blood	blood
27	chr1:224546200-224549400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:224546200-224550800	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:224546200-224551000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr1:224546200-224551200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:224546200-224551400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr1:224546200-224551400	Weak transcription	HSMMtube	muscle
33	chr1:224546200-224551800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:224546200-224552800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:224546200-224553000	Weak transcription	HSMM	muscle
36	chr1:224546200-224553200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:224546200-224553400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:224546200-224553600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:224546200-224554800	Weak transcription	Placenta	Placenta
40	chr1:224546200-224554800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:224546200-224555200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:224546200-224555200	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:224546200-224555200	Weak transcription	Brain Substantia Nigra	brain
44	chr1:224546200-224555200	Weak transcription	Colonic Mucosa	Colon
45	chr1:224546200-224555200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:224546200-224555200	Weak transcription	Right Ventricle	heart
47	chr1:224546200-224555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:224546400-224549400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:224546400-224551400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:224546400-224551600	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links