Variant report

Variant	rs12737233
Chromosome Location	chr1:70784935-70784936
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70783413..70785346-chr1:70819101..70821249,2	K562	blood:

Variant related genes	Relation type
ENSG00000118454	Chromatin interaction
ENSG00000197568	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10518334	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12139863	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs12565719	0.85[CEU][hapmap]
rs12725762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12741805	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34467894	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34778519	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs482291	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs490574	1.00[JPT][hapmap]
rs508310	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs542842	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs664051	0.85[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014292	chr1:70689215-70799065	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv1792702	chr1:70755511-70818576	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	nsv871430	chr1:70765659-70819912	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12737233	HHLA3	cis	parietal	SCAN
rs12737233	DIRAS3	cis	parietal	SCAN
rs12737233	HHLA3	cis	lymphoblastoid	seeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70688000-70819200	Weak transcription	Esophagus	oesophagus
2	chr1:70716800-70815800	Weak transcription	Brain Angular Gyrus	brain
3	chr1:70717800-70788200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:70734000-70786000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:70734400-70786000	Weak transcription	Psoas Muscle	Psoas
6	chr1:70734400-70813000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:70752800-70793400	Weak transcription	Gastric	stomach
8	chr1:70757000-70799800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:70757400-70813200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:70757800-70786000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:70757800-70799400	Weak transcription	Brain Germinal Matrix	brain
12	chr1:70757800-70812400	Weak transcription	Fetal Brain Male	brain
13	chr1:70759400-70785400	Weak transcription	HMEC	breast
14	chr1:70760200-70799800	Weak transcription	Lung	lung
15	chr1:70760400-70802400	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:70760400-70813200	Weak transcription	Fetal Brain Female	brain
17	chr1:70760600-70818200	Weak transcription	Aorta	Aorta
18	chr1:70760600-70818600	Weak transcription	Thymus	Thymus
19	chr1:70761800-70785400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:70762000-70817600	Weak transcription	NHLF	lung
21	chr1:70762200-70818200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:70765400-70799200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:70765600-70818200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:70765800-70788200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:70765800-70799400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:70765800-70812200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:70767400-70789800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:70767600-70785600	Weak transcription	NHDF-Ad	bronchial
29	chr1:70767600-70786600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:70767600-70788000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:70767600-70798600	Weak transcription	K562	blood
32	chr1:70767800-70785200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:70767800-70785200	Weak transcription	HUVEC	blood vessel
34	chr1:70767800-70785400	Weak transcription	NH-A	brain
35	chr1:70767800-70785600	Weak transcription	HSMM	muscle
36	chr1:70767800-70786600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:70767800-70789800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:70767800-70799200	Weak transcription	Placenta	Placenta
39	chr1:70767800-70819000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:70768000-70785600	Weak transcription	Hela-S3	cervix
41	chr1:70768200-70817000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr1:70768800-70787200	Weak transcription	GM12878-XiMat	blood
43	chr1:70770400-70809200	Weak transcription	Ovary	ovary
44	chr1:70770400-70817200	Weak transcription	Pancreas	Pancrea
45	chr1:70772400-70785200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:70773400-70799200	Weak transcription	HepG2	liver
47	chr1:70773600-70818200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr1:70773800-70786800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:70773800-70787400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:70773800-70818200	Weak transcription	Stomach Smooth Muscle	stomach

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