Variant report

Variant	rs936428
Chromosome Location	chr3:48167281-48167282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr3:48166192-48167593	IMR90	lung:	n/a	n/a
2	TCF7L2	chr3:48166559-48167374	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr3:48166413-48167430	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48160937..48162858-chr3:48166564..48169922,3	K562	blood:

Variant related genes	Relation type
ENSG00000236768	TF binding region
ENSG00000236768	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1013431	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10446426	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130152	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11130154	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130155	0.87[CEU][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11710866	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11714518	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11720151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11720973	0.80[EUR][1000 genomes]
rs12486714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12493348	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13074973	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13075457	0.81[EUR][1000 genomes]
rs13075795	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13080997	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13085054	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13089844	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1530646	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1550914	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2034963	0.96[EUR][1000 genomes]
rs2053767	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2121754	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2166770	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2166772	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2361683	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2361684	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28637561	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34597784	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35314534	0.82[EUR][1000 genomes]
rs35689209	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4293721	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4296617	0.82[EUR][1000 genomes]
rs4392441	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4599334	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858810	0.92[CEU][hapmap]
rs4858876	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858880	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4858881	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4858887	0.83[EUR][1000 genomes]
rs5012971	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442090	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6442091	0.82[EUR][1000 genomes]
rs6442101	0.96[CEU][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes]
rs6442102	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67536946	0.82[EUR][1000 genomes]
rs6766641	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6770467	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6770477	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6773208	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6777081	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6791834	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6793477	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6803741	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6804520	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6806820	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7374482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374516	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7426976	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7427418	0.88[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7427648	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7430879	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7430913	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7620736	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7627645	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7642590	0.96[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs7649981	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9811277	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9814961	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9825114	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes]
rs9846062	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9854454	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9860485	0.81[EUR][1000 genomes]
rs9862913	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking 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	21 gene(s)	inside rSNPs	diseases
3	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv1012828	chr3:47996472-48192862	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv876760	chr3:48019258-48197614	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv834681	chr3:48032000-48181775	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	34 gene(s)	inside rSNPs	diseases
11	nsv1012024	chr3:48119229-48242670	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv834682	chr3:48138137-48311122	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs936428	ZNF589	cis	Nerve Tibial	GTEx
rs936428	MRPS18AP1	cis	Thyroid	GTEx
rs936428	MRPS18AP1	cis	lung	GTEx
rs936428	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs936428	ZNF589	cis	Artery Tibial	GTEx
rs936428	MRPS18AP1	cis	Artery Tibial	GTEx
rs936428	ZNF589	cis	multi-tissue	Pritchard
rs936428	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs936428	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs936428	ZNF589	cis	Lymphoblastoid	GTEx
rs936428	MRPS18AP1	cis	Nerve Tibial	GTEx
rs936428	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs936428	CDC25A	cis	Muscle Skeletal	GTEx
rs936428	CDC25A	cis	Thyroid	GTEx
rs936428	ZNF589	cis	Esophagus Mucosa	GTEx
rs936428	NME6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48161200-48171200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:48164400-48172000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:48165200-48167600	Enhancers	Hela-S3	cervix
4	chr3:48165200-48171600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:48165400-48167800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:48166000-48167400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:48166000-48167800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:48166200-48167600	Enhancers	Adipose Nuclei	Adipose
9	chr3:48166400-48167400	Enhancers	NH-A	brain
10	chr3:48166400-48167600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:48166400-48167800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:48166400-48167800	Enhancers	Fetal Thymus	thymus
13	chr3:48166600-48167400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr3:48166600-48167400	Enhancers	Thymus	Thymus
15	chr3:48166600-48167400	Enhancers	NHLF	lung
16	chr3:48166600-48167600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:48166600-48167800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr3:48166800-48167400	Enhancers	H1 Cell Line	embryonic stem cell
19	chr3:48166800-48167400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:48166800-48167800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:48166800-48167800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:48166800-48167800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:48166800-48167800	Enhancers	GM12878-XiMat	blood
24	chr3:48167000-48171400	Weak transcription	Placenta	Placenta
25	chr3:48167000-48171400	Weak transcription	HepG2	liver
26	chr3:48167000-48171400	Weak transcription	HSMM	muscle
27	chr3:48167000-48177400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:48167200-48167400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:48167200-48167400	Enhancers	Stomach Smooth Muscle	stomach
30	chr3:48167200-48168000	Enhancers	Primary B cells from peripheral blood	blood
31	chr3:48167200-48170200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:48167200-48171200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:48167200-48171200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:48167200-48171200	Weak transcription	Ovary	ovary
35	chr3:48167200-48171200	Weak transcription	HSMMtube	muscle
36	chr3:48167200-48171200	Weak transcription	NHDF-Ad	bronchial
37	chr3:48167200-48171200	Weak transcription	Osteobl	bone
38	chr3:48167200-48178800	Weak transcription	NHEK	skin

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