Variant report

Variant	rs10799543
Chromosome Location	chr1:224413870-224413871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224410361..224412569-chr1:224413431..224415839,2	K562	blood:
2	chr1:224369827..224372734-chr1:224412910..224414820,2	K562	blood:
3	chr1:224410677..224413155-chr1:224413701..224415369,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143753	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10799491	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs10799507	0.88[EUR][1000 genomes]
rs10916458	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs10916462	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916472	0.88[EUR][1000 genomes]
rs10916481	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916497	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916498	0.96[EUR][1000 genomes]
rs12082619	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12083770	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120308	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124547	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126765	0.88[EUR][1000 genomes]
rs12126815	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12133599	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12138866	0.92[EUR][1000 genomes]
rs12140137	0.92[EUR][1000 genomes]
rs12184283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45583539	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60256604	0.88[EUR][1000 genomes]
rs6660194	0.88[EUR][1000 genomes]
rs6686449	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs6694451	1.00[CEU][hapmap]
rs6701036	0.81[EUR][1000 genomes]
rs68073536	0.96[EUR][1000 genomes]
rs72753956	0.88[EUR][1000 genomes]
rs72753969	0.88[EUR][1000 genomes]
rs72753980	0.80[EUR][1000 genomes]
rs72753994	0.88[EUR][1000 genomes]
rs72754000	0.92[EUR][1000 genomes]
rs72754001	0.85[EUR][1000 genomes]
rs72755905	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7514140	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7552239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10799543	CNIH4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224389600-224414400	Weak transcription	Fetal Brain Female	brain
2	chr1:224393800-224414200	Weak transcription	Colonic Mucosa	Colon
3	chr1:224394000-224414000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:224394000-224414600	Weak transcription	HMEC	breast
5	chr1:224398000-224414200	Weak transcription	Spleen	Spleen
6	chr1:224399400-224414200	Weak transcription	Adipose Nuclei	Adipose
7	chr1:224399400-224414200	Weak transcription	Brain Anterior Caudate	brain
8	chr1:224401400-224414800	Weak transcription	Right Ventricle	heart
9	chr1:224401600-224414400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:224401800-224415200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:224401800-224427600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:224401800-224475400	Weak transcription	Esophagus	oesophagus
13	chr1:224402200-224414200	Weak transcription	GM12878-XiMat	blood
14	chr1:224406000-224414200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr1:224406200-224414200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:224406200-224414200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:224406200-224414200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:224406200-224414200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:224406200-224414200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:224406200-224414200	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:224406200-224414400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:224406400-224414200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr1:224406800-224414400	Weak transcription	Pancreas	Pancrea
24	chr1:224407200-224414400	Weak transcription	Placenta	Placenta
25	chr1:224407600-224414200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:224407600-224414200	Weak transcription	Fetal Thymus	thymus
27	chr1:224407600-224414200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:224407600-224434000	Weak transcription	Fetal Brain Male	brain
29	chr1:224407800-224414200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:224407800-224414200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:224407800-224414200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:224408000-224414200	Weak transcription	Gastric	stomach
33	chr1:224410400-224414200	Weak transcription	Liver	Liver
34	chr1:224411400-224414200	Weak transcription	Brain Substantia Nigra	brain
35	chr1:224411400-224414200	Weak transcription	Fetal Intestine Large	intestine
36	chr1:224411400-224417400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:224411600-224414200	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:224411600-224414200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:224411600-224414200	Weak transcription	Left Ventricle	heart
40	chr1:224411600-224414400	Weak transcription	Aorta	Aorta
41	chr1:224411600-224414400	Weak transcription	HSMMtube	muscle
42	chr1:224411600-224414600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:224411600-224438000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr1:224411600-224454400	Weak transcription	Psoas Muscle	Psoas
45	chr1:224411800-224414200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:224411800-224414200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:224411800-224414400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr1:224412000-224414000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:224412000-224414200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:224412000-224414200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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