Variant report

Variant	rs6687643
Chromosome Location	chr1:224331124-224331125
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10916370	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11576702	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11582248	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11582460	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12410321	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12722938	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12736412	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12737029	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12739782	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12749977	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16844823	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16856443	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2008340	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2087795	0.84[ASN][1000 genomes]
rs35177633	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35243286	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35540939	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826374	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826409	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61827700	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6656849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6657195	0.84[ASN][1000 genomes]
rs71644775	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71644776	0.84[ASN][1000 genomes]
rs71644777	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9662363	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv873222	chr1:224292898-224335422	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224303000-224363400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:224314400-224333800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:224314400-224343400	Weak transcription	Psoas Muscle	Psoas
4	chr1:224315800-224331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:224316400-224331200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr1:224316600-224352200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:224317600-224333400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:224317800-224334000	Strong transcription	Fetal Intestine Large	intestine
9	chr1:224318000-224331200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:224318000-224332000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:224318200-224333400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:224318400-224331200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:224319200-224334000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:224319200-224335000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:224319800-224331200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:224320200-224344800	Weak transcription	Gastric	stomach
17	chr1:224320200-224345000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:224320200-224345000	Weak transcription	HUVEC	blood vessel
19	chr1:224320400-224344800	Weak transcription	Small Intestine	intestine
20	chr1:224320400-224345000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:224320400-224345000	Weak transcription	Right Ventricle	heart
22	chr1:224320400-224345200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:224320600-224344000	Weak transcription	Brain Germinal Matrix	brain
24	chr1:224320600-224345000	Weak transcription	Pancreas	Pancrea
25	chr1:224320600-224345200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:224320800-224339000	Weak transcription	A549	lung
27	chr1:224320800-224343200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:224320800-224344200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:224320800-224344800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr1:224320800-224345200	Weak transcription	Brain Substantia Nigra	brain
31	chr1:224321000-224337200	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:224321000-224338400	Weak transcription	Brain Angular Gyrus	brain
33	chr1:224321000-224343200	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:224321000-224343400	Weak transcription	Fetal Brain Male	brain
35	chr1:224321000-224344200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:224321000-224344800	Weak transcription	NHLF	lung
37	chr1:224321000-224345000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:224321000-224345400	Weak transcription	Fetal Heart	heart
39	chr1:224322000-224333400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:224322000-224345400	Weak transcription	HMEC	breast
41	chr1:224322400-224336200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:224322400-224337600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:224322600-224345000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:224322800-224331400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr1:224323000-224335400	Strong transcription	Fetal Intestine Small	intestine
46	chr1:224323000-224337000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:224323000-224337200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:224323000-224341000	Weak transcription	NH-A	brain
49	chr1:224323000-224343200	Weak transcription	NHDF-Ad	bronchial
50	chr1:224323200-224332200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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