Variant report

Variant	rs543860
Chromosome Location	chr1:70901853-70901854
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70900549..70904581-chr1:70906967..70911006,5	K562	blood:

Variant related genes	Relation type
ENSG00000271992	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10493473	0.82[EUR][1000 genomes]
rs11209612	0.80[EUR][1000 genomes]
rs11209613	0.80[EUR][1000 genomes]
rs1145920	0.99[ASN][1000 genomes]
rs12023001	0.81[ASN][1000 genomes]
rs12116830	0.80[EUR][1000 genomes]
rs12118663	0.82[EUR][1000 genomes]
rs12126226	0.82[EUR][1000 genomes]
rs12137720	0.82[EUR][1000 genomes]
rs12751638	0.82[EUR][1000 genomes]
rs35481139	0.82[EUR][1000 genomes]
rs3856027	0.81[ASN][1000 genomes]
rs475263	0.90[ASN][1000 genomes]
rs481654	0.99[ASN][1000 genomes]
rs482291	0.88[EUR][1000 genomes]
rs490574	0.88[EUR][1000 genomes]
rs501939	0.99[ASN][1000 genomes]
rs508310	0.88[EUR][1000 genomes]
rs513263	0.83[EUR][1000 genomes]
rs525276	1.00[ASN][1000 genomes]
rs542842	0.82[EUR][1000 genomes]
rs546503	0.81[EUR][1000 genomes]
rs559062	1.00[ASN][1000 genomes]
rs561926	0.88[EUR][1000 genomes]
rs596793	0.92[ASN][1000 genomes]
rs608609	0.99[ASN][1000 genomes]
rs618531	0.88[EUR][1000 genomes]
rs664051	0.88[EUR][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	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv461828	chr1:70880717-70922360	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv546456	chr1:70880717-70922360	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs543860	HHLA3	Cis_1M	lymphoblastoid	RTeQTL
rs543860	HHLA3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70877400-70903400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:70877400-70906400	Weak transcription	Small Intestine	intestine
3	chr1:70877400-70906600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:70877800-70907800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:70878000-70903400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:70878000-70908200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:70878200-70907000	Weak transcription	Psoas Muscle	Psoas
8	chr1:70878200-70909600	Weak transcription	Gastric	stomach
9	chr1:70878400-70907000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:70878600-70902600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:70878600-70903800	Weak transcription	HSMMtube	muscle
12	chr1:70878600-70906000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:70878800-70902200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:70884400-70909000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:70884600-70902800	Weak transcription	Osteobl	bone
16	chr1:70886400-70906600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:70886400-70906800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:70888000-70906000	Weak transcription	Fetal Brain Male	brain
19	chr1:70891400-70907400	Weak transcription	Fetal Stomach	stomach
20	chr1:70892200-70907400	Weak transcription	Fetal Brain Female	brain
21	chr1:70892400-70906400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:70892600-70906200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr1:70893000-70903200	Weak transcription	HMEC	breast
24	chr1:70893200-70907800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:70894000-70906200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:70894400-70906600	Weak transcription	Fetal Heart	heart
27	chr1:70894600-70905200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:70895400-70905600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:70895400-70906200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:70895400-70907000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:70895600-70905400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:70895800-70912000	Weak transcription	Hela-S3	cervix
33	chr1:70896000-70902200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:70896000-70905400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:70896000-70905800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:70896400-70904400	Weak transcription	HSMM	muscle
37	chr1:70896400-70905000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:70896600-70902200	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr1:70896600-70902200	Strong transcription	Ovary	ovary
40	chr1:70896600-70902600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:70896600-70902600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:70896600-70905800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:70896800-70905000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:70897000-70909600	Weak transcription	Pancreas	Pancrea
45	chr1:70897600-70902200	Strong transcription	Left Ventricle	heart
46	chr1:70897600-70904600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:70897800-70902000	Strong transcription	Fetal Muscle Leg	muscle
48	chr1:70897800-70902600	Weak transcription	Colon Smooth Muscle	Colon
49	chr1:70897800-70902800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:70897800-70903200	Strong transcription	Brain Substantia Nigra	brain

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