Variant report

Variant	rs3820624
Chromosome Location	chr1:228268492-228268493
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228267816..228271023-chr1:228334433..228337364,3	K562	blood:
2	chr1:228192379..228197446-chr1:228268248..228273367,9	MCF-7	breast:
3	chr1:228268335..228271224-chr1:228352172..228356089,4	K562	blood:
4	chr1:228267983..228269550-chr1:228473871..228475607,2	K562	blood:
5	chr1:228180647..228182707-chr1:228268126..228270057,2	K562	blood:
6	chr1:228266682..228273620-chr1:228293839..228298603,9	MCF-7	breast:
7	chr1:228216833..228219202-chr1:228268164..228269847,2	K562	blood:
8	chr1:228267667..228275106-chr1:228326600..228331394,10	K562	blood:
9	chr1:228267482..228269833-chr1:228325846..228328403,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000154342	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000143774	Chromatin interaction
ENSG00000162910	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1034792	0.82[EUR][1000 genomes]
rs1048503	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916262	0.81[AMR][1000 genomes]
rs10916266	0.81[ASN][1000 genomes]
rs1094603	0.81[ASN][1000 genomes]
rs11582265	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11582704	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11584499	0.97[ASN][1000 genomes]
rs11589513	0.81[AMR][1000 genomes]
rs1188975	0.91[EUR][1000 genomes]
rs1188977	0.98[EUR][1000 genomes]
rs12033088	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12048010	0.81[AMR][1000 genomes]
rs1620734	0.98[EUR][1000 genomes]
rs1745422	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070960	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295995	0.84[EUR][1000 genomes]
rs3738680	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738681	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768329	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3768330	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41270175	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41270177	0.82[EUR][1000 genomes]
rs4653897	0.82[EUR][1000 genomes]
rs57146523	0.81[AMR][1000 genomes]
rs61825130	0.81[AMR][1000 genomes]
rs61825131	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61825133	0.99[ASN][1000 genomes]
rs61825135	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61825156	0.86[ASN][1000 genomes]
rs708126	0.91[EUR][1000 genomes]
rs72756204	0.81[AMR][1000 genomes]
rs72756209	0.81[AMR][1000 genomes]
rs822727	0.98[EUR][1000 genomes]
rs860301	0.98[EUR][1000 genomes]
rs882451	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3820624	MIXL1	cis	cerebellum	SCAN
rs3820624	OBSCN	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228248200-228269000	Weak transcription	Right Atrium	heart
2	chr1:228258600-228269000	Weak transcription	Esophagus	oesophagus
3	chr1:228260200-228269000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:228261600-228269000	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:228262200-228268800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:228263000-228268800	Weak transcription	Adipose Nuclei	Adipose
7	chr1:228263000-228269200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:228263600-228268800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:228263800-228269200	Weak transcription	Fetal Lung	lung
10	chr1:228264000-228268800	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:228264800-228268800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:228265000-228268800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:228265000-228268800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:228265200-228269000	Weak transcription	NHLF	lung
15	chr1:228265400-228268800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:228265600-228268800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:228265600-228268800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:228265600-228268800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:228265600-228269000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:228265600-228269000	Weak transcription	A549	lung
21	chr1:228265800-228268600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:228265800-228269000	Weak transcription	Fetal Intestine Small	intestine
23	chr1:228266000-228268600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:228266000-228268800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:228266000-228269000	Weak transcription	Lung	lung
26	chr1:228266000-228269200	Weak transcription	Left Ventricle	heart
27	chr1:228266200-228268800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:228266200-228268800	Weak transcription	HUVEC	blood vessel
29	chr1:228266400-228269000	Weak transcription	NHEK	skin
30	chr1:228266800-228269000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:228266800-228269000	Enhancers	Primary T cells fromperipheralblood	blood
32	chr1:228267000-228269000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:228267000-228269200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr1:228267000-228269200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:228267200-228269000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:228267400-228269000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:228267600-228268600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:228267600-228268800	Enhancers	Dnd41	blood
39	chr1:228267600-228268800	Enhancers	GM12878-XiMat	blood
40	chr1:228267600-228269000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:228267600-228269000	Weak transcription	Fetal Stomach	stomach
42	chr1:228267800-228268800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:228267800-228268800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:228267800-228268800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:228267800-228269000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:228267800-228269000	Weak transcription	Spleen	Spleen
47	chr1:228267800-228269200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:228268000-228268800	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr1:228268000-228269000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:228268000-228269000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links