Variant report

Variant	rs12642735
Chromosome Location	chr4:120524620-120524621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10012485	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10021460	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10022664	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518335	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12502511	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12503853	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12646525	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12648259	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13115778	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1987179	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2248236	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2389863	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2389864	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2389866	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2389869	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2622499	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2622500	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28382361	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28412979	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28540362	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28564258	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28566610	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28610991	0.84[ASN][1000 genomes]
rs28625289	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650385	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2892867	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2928993	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2928994	0.83[EUR][1000 genomes]
rs3733526	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756154	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3756157	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4337718	0.82[EUR][1000 genomes]
rs4597811	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4626181	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833622	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834784	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6534146	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534147	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6822275	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6834347	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6842674	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6847164	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7659250	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7670921	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7672961	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7681796	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684899	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9998919	0.89[EUR][1000 genomes];0.88[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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12642735	RP11-33B1.1	cis	Thyroid	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120486800-120527600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:120492200-120540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:120502200-120527800	Weak transcription	Pancreas	Pancrea
4	chr4:120502400-120526400	Weak transcription	Fetal Stomach	stomach
5	chr4:120502600-120541000	Weak transcription	Left Ventricle	heart
6	chr4:120506200-120525800	Weak transcription	Fetal Kidney	kidney
7	chr4:120512600-120530400	Weak transcription	Colonic Mucosa	Colon
8	chr4:120512800-120531600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:120514200-120528600	Weak transcription	Gastric	stomach
10	chr4:120516800-120527800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:120517000-120527600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:120517000-120527800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:120517000-120531400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:120517000-120536600	Weak transcription	Ovary	ovary
15	chr4:120518800-120547200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:120519000-120533400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:120519600-120528600	Strong transcription	Osteobl	bone
18	chr4:120519800-120527600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:120519800-120527800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr4:120520200-120525000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:120520200-120525200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:120520200-120525200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:120520200-120525200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:120520200-120527800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:120520200-120527800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:120520200-120529800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr4:120520200-120536400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:120520400-120525400	Weak transcription	Small Intestine	intestine
29	chr4:120520400-120525800	Weak transcription	Psoas Muscle	Psoas
30	chr4:120520400-120533200	Weak transcription	Fetal Intestine Small	intestine
31	chr4:120520400-120537600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr4:120520600-120527800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr4:120520600-120529600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:120520800-120527600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:120520800-120527800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr4:120520800-120529400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:120521000-120529800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:120521000-120544800	Weak transcription	Fetal Intestine Large	intestine
39	chr4:120521200-120527400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:120521400-120527800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr4:120522000-120530400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:120523000-120527800	Weak transcription	Aorta	Aorta
43	chr4:120523000-120527800	Weak transcription	Lung	lung
44	chr4:120524000-120525600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:120524000-120526400	Enhancers	Colon Smooth Muscle	Colon
46	chr4:120524000-120528400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:120524400-120524800	Enhancers	Fetal Heart	heart
48	chr4:120524600-120525000	Weak transcription	Fetal Muscle Leg	muscle
49	chr4:120524600-120525400	Weak transcription	NHLF	lung
50	chr4:120524600-120525600	Weak transcription	Fetal Lung	lung

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