Variant report

Variant	rs12119007
Chromosome Location	chr1:247218227-247218228
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1007457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10493861	0.90[CHB][hapmap]
rs10754536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10802463	0.95[ASN][1000 genomes]
rs10802466	1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[ASN][1000 genomes]
rs10802468	0.81[ASN][1000 genomes]
rs10802469	0.81[ASN][1000 genomes]
rs10924907	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10924909	0.88[ASN][1000 genomes]
rs10924910	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[ASN][1000 genomes]
rs10924912	0.82[ASN][1000 genomes]
rs10924914	0.81[ASN][1000 genomes]
rs10924919	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12084753	0.88[ASN][1000 genomes]
rs12093759	0.90[CHB][hapmap]
rs12094740	0.88[ASN][1000 genomes]
rs12119918	0.81[ASN][1000 genomes]
rs12121335	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12122715	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12127349	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12129591	0.95[ASN][1000 genomes]
rs12133296	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12133763	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs12140839	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12141797	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12141826	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12142274	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12144733	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12691533	0.86[ASN][1000 genomes]
rs12723583	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12740588	0.94[ASN][1000 genomes]
rs12751386	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13376442	0.88[ASN][1000 genomes]
rs1552988	0.88[ASN][1000 genomes]
rs166643	0.94[ASN][1000 genomes]
rs1874407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs192432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2055190	0.89[ASN][1000 genomes]
rs2055193	0.91[ASN][1000 genomes]
rs2172795	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2255481	0.88[ASN][1000 genomes]
rs2270616	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2379192	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2379193	0.88[ASN][1000 genomes]
rs2642962	0.94[ASN][1000 genomes]
rs273378	0.95[ASN][1000 genomes]
rs2818880	0.94[ASN][1000 genomes]
rs2890101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2890102	0.88[ASN][1000 genomes]
rs2890103	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2890104	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2890105	0.88[ASN][1000 genomes]
rs2890106	0.88[ASN][1000 genomes]
rs34060714	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34225777	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34273666	0.88[ASN][1000 genomes]
rs34350972	0.88[ASN][1000 genomes]
rs34764574	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34870081	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34919391	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35314391	0.88[ASN][1000 genomes]
rs35452630	0.88[ASN][1000 genomes]
rs35511369	0.88[ASN][1000 genomes]
rs3736325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3806269	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3844079	0.90[CHB][hapmap]
rs3844080	0.90[CHB][hapmap]
rs3892246	0.88[ASN][1000 genomes]
rs3892516	0.88[ASN][1000 genomes]
rs41305955	0.91[ASN][1000 genomes]
rs4622098	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925692	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs57003817	0.88[ASN][1000 genomes]
rs60293371	0.88[ASN][1000 genomes]
rs60677310	0.88[ASN][1000 genomes]
rs60794525	0.88[ASN][1000 genomes]
rs6426209	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6426218	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6426220	0.90[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs6658298	0.89[ASN][1000 genomes]
rs6659256	0.88[ASN][1000 genomes]
rs6664157	0.89[ASN][1000 genomes]
rs6669242	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6675536	0.90[CHB][hapmap]
rs6676355	0.92[ASN][1000 genomes]
rs6677000	0.97[ASN][1000 genomes]
rs6681227	0.86[ASN][1000 genomes]
rs6685921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6693464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6695894	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6699898	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6702419	0.86[ASN][1000 genomes]
rs7412787	0.89[ASN][1000 genomes]
rs7518407	0.97[ASN][1000 genomes]
rs7521596	0.90[CHB][hapmap]
rs7528817	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs7549674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9793102	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1000602	chr1:247044627-247226568	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
8	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
9	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
10	nsv999879	chr1:247112207-247276918	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
12	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
13	nsv873427	chr1:247140425-247218227	ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv1012616	chr1:247173851-247365588	Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
15	nsv535420	chr1:247173851-247365588	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
16	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers 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	30 gene(s)	inside rSNPs	diseases
17	nsv999352	chr1:247180668-247307074	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
18	nsv535421	chr1:247180668-247307074	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
19	nsv997687	chr1:247180668-247348847	Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
20	nsv535422	chr1:247180668-247348847	ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
21	nsv427974	chr1:247184802-247352964	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
22	esv3336179	chr1:247195262-247373269	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
23	nsv533111	chr1:247200511-247264759	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
24	nsv1014012	chr1:247207932-247289138	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12119007	ZNF124	cis	lymphoblastoid	seeQTL
rs12119007	ZNF670	cis	parietal	SCAN
rs12119007	ZNF124	cis	parietal	SCAN
rs12119007	ZNF695	cis	cerebellum	SCAN
rs12119007	ZNF670	cis	Liver	GTEx
rs12119007	ZNF124	cis	cerebellum	SCAN
rs12119007	C1orf229	cis	cerebellum	SCAN
rs12119007	ZNF670	cis	cerebellum	SCAN
rs12119007	ZNF670	trans	multi-tissue	Pritchard
rs12119007	ZNF670	Cis_1M	lymphoblastoid	RTeQTL
rs12119007	ZNF669	cis	cerebellum	SCAN
rs12119007	ZNF669	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247196600-247219400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
2	chr1:247201600-247218400	Weak transcription	Right Ventricle	heart
3	chr1:247213200-247221000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:247215200-247219200	ZNF genes & repeats	Liver	Liver
5	chr1:247215200-247220600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
6	chr1:247215200-247222200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:247215400-247219000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
8	chr1:247215400-247219000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr1:247215400-247219200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:247215400-247221200	ZNF genes & repeats	Dnd41	blood
11	chr1:247215600-247218600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:247215600-247218800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:247215600-247218800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
14	chr1:247215600-247218800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr1:247215800-247218400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr1:247217000-247219400	Enhancers	HepG2	liver
17	chr1:247217200-247219000	Enhancers	Stomach Mucosa	stomach
18	chr1:247217200-247219000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr1:247217400-247218800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:247217600-247219000	ZNF genes & repeats	Adipose Nuclei	Adipose
21	chr1:247217800-247218800	Enhancers	Stomach Smooth Muscle	stomach
22	chr1:247217800-247219600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:247218200-247218600	Enhancers	HSMMtube	muscle
24	chr1:247218200-247218800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
25	chr1:247218200-247218800	Enhancers	HUVEC	blood vessel
26	chr1:247218200-247218800	Enhancers	K562	blood

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