Variant report

Variant	rs12489110
Chromosome Location	chr3:121435001-121435002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10934556	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10934557	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934561	0.81[AFR][1000 genomes]
rs11915822	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919421	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488717	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489196	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491671	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12491714	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12492214	0.81[AFR][1000 genomes]
rs12492861	0.81[AFR][1000 genomes]
rs12493927	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12631803	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636562	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12637265	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1574654	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1814668	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1919553	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919554	0.85[ASN][1000 genomes]
rs1919556	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971281	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2055034	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2222826	0.81[AFR][1000 genomes]
rs34241542	0.81[AFR][1000 genomes]
rs35354585	0.81[AFR][1000 genomes]
rs35674179	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35825165	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3966063	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4048693	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271407	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs55930520	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55964762	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56109033	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56286202	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58485759	0.81[AFR][1000 genomes]
rs59064186	0.81[AFR][1000 genomes]
rs59228534	0.81[AFR][1000 genomes]
rs6762575	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6766737	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775634	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786605	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793556	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798575	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7643293	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12489110	HCLS1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121386600-121447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:121396800-121435600	Weak transcription	Psoas Muscle	Psoas
3	chr3:121399000-121440400	Weak transcription	K562	blood
4	chr3:121410400-121435600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:121411000-121442400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:121411400-121437200	Weak transcription	Small Intestine	intestine
7	chr3:121413400-121446200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:121414800-121436200	Weak transcription	Stomach Mucosa	stomach
9	chr3:121417200-121435800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:121417600-121435200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:121417600-121437200	Weak transcription	Spleen	Spleen
12	chr3:121418000-121435400	Weak transcription	NHLF	lung
13	chr3:121418800-121442000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:121419600-121436200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:121421200-121435200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:121421400-121436600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr3:121421400-121436600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:121424600-121435400	Weak transcription	Right Ventricle	heart
19	chr3:121426200-121442600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:121426200-121443200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:121427000-121436600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:121427400-121435400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:121428600-121438200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:121428800-121436400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr3:121429000-121450000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr3:121429400-121442800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:121429400-121448800	Strong transcription	Primary hematopoietic stem cells	blood
28	chr3:121429400-121449000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:121429600-121435400	Weak transcription	Esophagus	oesophagus
30	chr3:121430200-121442400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:121430200-121450000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:121430400-121436600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:121430400-121441400	Strong transcription	Osteobl	bone
34	chr3:121430600-121449000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:121430600-121449400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:121430600-121450000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr3:121430800-121438000	Strong transcription	Brain Hippocampus Middle	brain
38	chr3:121430800-121443600	Strong transcription	Placenta	Placenta
39	chr3:121430800-121448200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:121430800-121448800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:121430800-121448800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:121430800-121450000	Strong transcription	Fetal Intestine Large	intestine
43	chr3:121431000-121441000	Strong transcription	HepG2	liver
44	chr3:121431000-121442400	Strong transcription	GM12878-XiMat	blood
45	chr3:121431000-121444800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr3:121431000-121448600	Strong transcription	Adipose Nuclei	Adipose
47	chr3:121431000-121449000	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:121431000-121449000	Strong transcription	Fetal Thymus	thymus
49	chr3:121431000-121449600	Strong transcription	Liver	Liver
50	chr3:121431000-121450000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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