Variant report

Variant	rs12140479
Chromosome Location	chr1:70823238-70823239
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12137720	0.88[JPT][hapmap];0.85[YRI][hapmap]
rs12730494	0.83[AFR][1000 genomes]
rs12732737	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7536099	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[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	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
5	esv11736	chr1:70820591-70825114	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12140479	HHLA3	cis	Esophagus Muscularis	GTEx
rs12140479	HHLA3	Cis_1M	lymphoblastoid	RTeQTL
rs12140479	HHLA3	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70821000-70824000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:70821000-70827600	Weak transcription	HSMM	muscle
3	chr1:70821000-70835200	Weak transcription	Pancreas	Pancrea
4	chr1:70821000-70836400	Weak transcription	Left Ventricle	heart
5	chr1:70821000-70838400	Weak transcription	Lung	lung
6	chr1:70821200-70823800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:70821200-70824200	Weak transcription	HMEC	breast
8	chr1:70821200-70824200	Weak transcription	NHLF	lung
9	chr1:70821200-70824400	Weak transcription	NHEK	skin
10	chr1:70821200-70824600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:70821200-70827600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:70821200-70828000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:70821200-70829600	Weak transcription	Fetal Intestine Small	intestine
14	chr1:70821200-70832000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:70821200-70833600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:70821200-70835200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:70821200-70836800	Weak transcription	Fetal Stomach	stomach
18	chr1:70821200-70841400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:70821400-70824600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:70821400-70827000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:70821400-70827400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:70821400-70827400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:70821400-70827600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:70821400-70827600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:70821400-70827600	Weak transcription	Fetal Lung	lung
26	chr1:70821400-70827800	Weak transcription	Small Intestine	intestine
27	chr1:70821400-70832600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:70821400-70832600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:70821400-70838000	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:70821600-70823400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:70821600-70824000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:70821600-70828200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:70821600-70834800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:70821600-70836400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:70821600-70839000	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:70822000-70824000	Weak transcription	GM12878-XiMat	blood
37	chr1:70822000-70827400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:70822000-70827600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:70822000-70827600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:70822000-70829000	Weak transcription	Brain Anterior Caudate	brain
41	chr1:70822000-70834000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:70822000-70836400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:70822000-70839400	Weak transcription	Brain Substantia Nigra	brain
44	chr1:70822200-70829400	Weak transcription	K562	blood
45	chr1:70822200-70835600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:70822400-70834600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:70823000-70823400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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