Variant report

Variant	rs12239114
Chromosome Location	chr1:155322142-155322143
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	chr1:155315148..155317637-chr1:155321614..155323848,2	K562	blood:
2	chr1:155315148..155318392-chr1:155319854..155323114,3	K562	blood:

Variant related genes	Relation type
ENSG00000116539	Chromatin interaction
ENSG00000207720	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10752611	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[TSI][hapmap]
rs10796943	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.96[LWK][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10796945	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs10796946	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10908463	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap]
rs10908465	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10908466	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10908467	0.80[EUR][1000 genomes]
rs10908469	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264359	0.84[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs11264361	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap]
rs11264362	0.94[ASN][1000 genomes]
rs11264363	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.96[ASN][1000 genomes]
rs11264366	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11264369	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11264370	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11264371	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs11264372	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs11264374	0.81[EUR][1000 genomes]
rs11264375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs11264380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap]
rs12021631	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12024696	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12025532	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12026638	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12028416	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12037824	0.83[AFR][1000 genomes]
rs12041534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs12046473	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12049455	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12067371	0.81[EUR][1000 genomes]
rs12079134	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12081067	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12131079	0.98[ASN][1000 genomes]
rs12143948	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs12239100	0.80[EUR][1000 genomes]
rs12724079	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs12746592	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap]
rs1325908	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs1360554	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs1886905	0.96[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs2025669	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2297480	0.88[CEU][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap]
rs35615695	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs4492610	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs5005770	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56675301	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6677385	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6684889	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs6688636	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs6692183	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66923802	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696888	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs71517782	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7416976	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7556102	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
4	esv1799856	chr1:155305059-155534616	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking 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 miRNA target site	41 gene(s)	inside rSNPs	diseases
5	esv1795662	chr1:155305059-155540660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS 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 miRNA target site	41 gene(s)	inside rSNPs	diseases
6	esv3369240	chr1:155322041-155322441	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12239114	THEM5	cis	parietal	SCAN
rs12239114	SETDB1	cis	parietal	SCAN
rs12239114	YY1AP1	cis	parietal	SCAN
rs12239114	GBAP1	cis	parietal	SCAN
rs12239114	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs12239114	YY1AP1	cis	cerebellum	SCAN
rs12239114	SPRR2A	cis	cerebellum	SCAN
rs12239114	GBA	cis	Esophagus Mucosa	GTEx
rs12239114	SPRR2D	cis	parietal	SCAN
rs12239114	GBAP1	cis	Artery Tibial	GTEx
rs12239114	RIT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155296000-155334400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:155296200-155349400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:155296600-155348200	Strong transcription	Fetal Stomach	stomach
4	chr1:155296800-155330000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:155297000-155330800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:155297200-155322600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:155297800-155357400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:155299600-155330200	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr1:155299600-155341200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr1:155299600-155353600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:155301200-155332200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:155301800-155334800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:155302400-155341200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:155302600-155330800	Strong transcription	Placenta	Placenta
15	chr1:155303000-155328000	Strong transcription	Primary T cells from cord blood	blood
16	chr1:155303000-155330400	Strong transcription	Stomach Smooth Muscle	stomach
17	chr1:155303000-155331200	Strong transcription	Fetal Muscle Trunk	muscle
18	chr1:155303000-155332200	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:155303000-155334400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:155303000-155341200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:155303000-155352800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:155303200-155330800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:155303200-155341000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:155303400-155332600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:155303600-155332200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:155304200-155332000	Strong transcription	Dnd41	blood
27	chr1:155304400-155330200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:155304400-155330800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr1:155304400-155331000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:155304400-155337200	Strong transcription	Fetal Muscle Leg	muscle
31	chr1:155304600-155326000	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:155304600-155330200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:155304600-155331800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:155304600-155332000	Strong transcription	Duodenum Mucosa	Duodenum
35	chr1:155306000-155324200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:155306000-155336800	Strong transcription	Adipose Nuclei	Adipose
37	chr1:155306000-155348200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:155306200-155330200	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:155306200-155330800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr1:155306200-155341200	Strong transcription	Liver	Liver
41	chr1:155306200-155375400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr1:155306400-155329800	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr1:155306400-155330800	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr1:155306400-155334600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:155306600-155324800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:155306600-155325400	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:155306600-155325600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:155306600-155332000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:155306600-155332200	Strong transcription	Fetal Intestine Large	intestine
50	chr1:155306600-155332600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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