Variant report

Variant	rs2348683
Chromosome Location	chr22:30002130-30002131
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29991169..29993450-chr22:30000929..30002699,2	K562	blood:
2	chr22:29998126..30001095-chr22:30001149..30002674,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186575	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1058642	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11090569	0.81[EUR][1000 genomes]
rs12172347	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12484392	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13054618	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13055568	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13055746	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13056992	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13057041	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800538	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1807506	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2024116	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024119	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024121	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240638	0.81[EUR][1000 genomes]
rs2267147	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2348672	0.80[EUR][1000 genomes]
rs2348677	0.80[EUR][1000 genomes]
rs2348684	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34013089	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35404981	0.80[EUR][1000 genomes]
rs3940296	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4470427	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67292640	0.81[EUR][1000 genomes]
rs67884471	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715490	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7287318	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs737980	0.80[EUR][1000 genomes]
rs737981	0.80[EUR][1000 genomes]
rs8142111	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs867088	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9608781	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9608785	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608787	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608789	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608790	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608794	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608798	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608799	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613940	0.80[EUR][1000 genomes]
rs9613942	0.80[EUR][1000 genomes]
rs9613943	0.80[EUR][1000 genomes]
rs9613956	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613957	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613958	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9613961	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9613963	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9613965	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9613970	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613971	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613975	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613977	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613978	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613979	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613980	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9613983	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9613984	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613986	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613990	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613991	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613992	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9613993	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613994	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613995	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9613996	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613997	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9613998	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9613999	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9614004	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614006	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614011	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614014	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614018	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999458	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS 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	16 gene(s)	inside rSNPs	diseases
9	nsv817417	chr22:29998464-30035142	Strong transcription Weak transcription Enhancers Flanking Active TSS 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	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2348683	THOC5	cis	Artery Tibial	GTEx
rs2348683	THOC5	cis	Thyroid	GTEx
rs2348683	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs2348683	THOC5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30000400-30002400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr22:30000400-30002600	Enhancers	Spleen	Spleen
3	chr22:30000400-30002800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr22:30000400-30003000	Enhancers	Pancreas	Pancrea
5	chr22:30000400-30026600	Weak transcription	Gastric	stomach
6	chr22:30000600-30002800	Enhancers	Placenta	Placenta
7	chr22:30000800-30002800	Enhancers	Left Ventricle	heart
8	chr22:30000800-30002800	Enhancers	Lung	lung
9	chr22:30001000-30002200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr22:30001000-30002200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr22:30001000-30002200	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr22:30001000-30002400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr22:30001000-30002400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr22:30001000-30002400	Weak transcription	Stomach Mucosa	stomach
15	chr22:30001000-30002600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr22:30001000-30002600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr22:30001000-30002600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr22:30001000-30002600	Enhancers	Colon Smooth Muscle	Colon
19	chr22:30001000-30002800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr22:30001000-30004800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr22:30001000-30013400	Weak transcription	Fetal Kidney	kidney
22	chr22:30001000-30019400	Weak transcription	Thymus	Thymus
23	chr22:30001200-30002200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr22:30001200-30002200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr22:30001200-30002400	Enhancers	Adipose Nuclei	Adipose
26	chr22:30001200-30002800	Enhancers	HepG2	liver
27	chr22:30001200-30004600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr22:30001200-30005400	Weak transcription	Aorta	Aorta
29	chr22:30001200-30006600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr22:30001200-30013800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr22:30001400-30002200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr22:30001400-30002200	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr22:30001400-30002400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr22:30001400-30002400	Weak transcription	Esophagus	oesophagus
35	chr22:30001400-30002600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr22:30001400-30003400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr22:30001400-30003600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr22:30001400-30003600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr22:30001400-30003800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr22:30001400-30004800	Weak transcription	Primary B cells from cord blood	blood
41	chr22:30001400-30005200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr22:30001400-30005800	Weak transcription	Fetal Intestine Large	intestine
43	chr22:30001400-30006600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr22:30001400-30013400	Weak transcription	Brain Angular Gyrus	brain
45	chr22:30001400-30013400	Weak transcription	Ovary	ovary
46	chr22:30001400-30013400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr22:30001400-30014000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr22:30001600-30002200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
49	chr22:30001600-30002200	Genic enhancers	Fetal Brain Female	brain
50	chr22:30001600-30002400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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