Variant report

Variant	rs12730494
Chromosome Location	chr1:70828243-70828244
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr1:70827297-70828431	H1-neurons	neurons:	n/a	n/a
2	GATA3	chr1:70827505-70828347	SK-N-SH	brain:	n/a	chr1:70827999-70828009

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70818807..70821510-chr1:70827045..70829382,2	MCF-7	breast:
2	chr1:70819013..70822302-chr1:70824014..70829303,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226088	TF binding region
ENSG00000197568	Chromatin interaction
ENSG00000118454	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10493473	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11209612	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11209613	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12116830	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12118663	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12126226	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12137720	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140479	0.83[AFR][1000 genomes]
rs12732737	0.81[AFR][1000 genomes]
rs12741941	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12751638	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35481139	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs482291	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs490574	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs508310	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs513263	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs542842	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs561926	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs618531	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs664051	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71500608	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71651454	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1012563	chr1:70753332-70832118	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1801665	chr1:70755511-70832053	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12730494	HHLA3	Cis_1M	lymphoblastoid	RTeQTL
rs12730494	HHLA3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70821000-70835200	Weak transcription	Pancreas	Pancrea
2	chr1:70821000-70836400	Weak transcription	Left Ventricle	heart
3	chr1:70821000-70838400	Weak transcription	Lung	lung
4	chr1:70821200-70829600	Weak transcription	Fetal Intestine Small	intestine
5	chr1:70821200-70832000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:70821200-70833600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:70821200-70835200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:70821200-70836800	Weak transcription	Fetal Stomach	stomach
9	chr1:70821200-70841400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:70821400-70832600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:70821400-70832600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:70821400-70838000	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:70821600-70834800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:70821600-70836400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:70821600-70839000	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:70822000-70829000	Weak transcription	Brain Anterior Caudate	brain
17	chr1:70822000-70834000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:70822000-70836400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:70822000-70839400	Weak transcription	Brain Substantia Nigra	brain
20	chr1:70822200-70829400	Weak transcription	K562	blood
21	chr1:70822200-70835600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:70822400-70834600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:70824800-70833000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:70825000-70836800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:70826000-70832600	Weak transcription	HMEC	breast
26	chr1:70826000-70833000	Weak transcription	Liver	Liver
27	chr1:70826200-70832600	Weak transcription	NHEK	skin
28	chr1:70826600-70832600	Weak transcription	Ovary	ovary
29	chr1:70827200-70828400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:70827200-70829200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:70827400-70828400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr1:70827400-70828400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:70827400-70829600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:70827600-70828400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:70827600-70828600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:70827600-70828600	Enhancers	HUVEC	blood vessel
37	chr1:70827800-70838400	Weak transcription	Fetal Lung	lung
38	chr1:70827800-70839800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr1:70828000-70829400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:70828000-70838200	Weak transcription	Adipose Nuclei	Adipose
41	chr1:70828200-70828400	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr1:70828200-70828400	Enhancers	Fetal Muscle Trunk	muscle

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