Variant report

Variant	rs12116830
Chromosome Location	chr1:70837827-70837828
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70820173..70823357-chr1:70837033..70840009,3	K562	blood:

Variant related genes	Relation type
ENSG00000197568	Chromatin interaction
ENSG00000118454	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10493473	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11209612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11209613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12118663	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12126226	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137720	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730494	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12741941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12751638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35481139	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482291	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs490574	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs508310	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs513263	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs542842	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs543860	0.80[EUR][1000 genomes]
rs561926	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs618531	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs664051	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71500608	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71651454	0.88[AMR][1000 genomes];0.96[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12116830	HHLA3	Cis_1M	lymphoblastoid	RTeQTL
rs12116830	HHLA3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70821000-70838400	Weak transcription	Lung	lung
2	chr1:70821200-70841400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:70821400-70838000	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:70821600-70839000	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:70822000-70839400	Weak transcription	Brain Substantia Nigra	brain
6	chr1:70827800-70838400	Weak transcription	Fetal Lung	lung
7	chr1:70827800-70839800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:70828000-70838200	Weak transcription	Adipose Nuclei	Adipose
9	chr1:70828400-70841000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:70829200-70838000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:70835400-70838200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:70835400-70838400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:70835400-70838400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:70835400-70838400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:70835400-70838600	Weak transcription	Liver	Liver
16	chr1:70835400-70838800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:70836400-70838600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:70837200-70838400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr1:70837200-70838800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:70837200-70839600	Weak transcription	Left Ventricle	heart
21	chr1:70837200-70846600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:70837800-70838000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:70837800-70838400	Strong transcription	Ovary	ovary

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