Variant report

Variant	rs339726
Chromosome Location	chr3:42697286-42697287
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	ZBTB7A	chr3:42694819-42697395	ECC-1	luminal epithelium:	n/a	chr3:42697295-42697303
2	EBF1	chr3:42696838-42697307	GM12878	blood:	n/a	n/a
3	ELF1	chr3:42696788-42697367	GM12878	blood:	n/a	chr3:42697127-42697136
4	STAT3	chr3:42696940-42697292	MCF10A-Er-Src	breast:	n/a	chr3:42697128-42697137 chr3:42697123-42697143 chr3:42697129-42697137 chr3:42697129-42697138 chr3:42697123-42697143 chr3:42697127-42697138
5	TCF12	chr3:42694130-42697494	ECC-1	luminal epithelium:	n/a	chr3:42694507-42694514 chr3:42697092-42697099 chr3:42694856-42694865
6	MAX	chr3:42696170-42697377	ECC-1	luminal epithelium:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42697183-42697193 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
7	MAZ	chr3:42692512-42697572	IMR90	lung:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42697183-42697193 chr3:42693401-42693411 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
8	EP300	chr3:42696882-42697452	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr3:42697097-42697320	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr3:42696079-42697377	U87	brain:	n/a	n/a
11	NFIC	chr3:42696305-42697519	ECC-1	luminal epithelium:	n/a	chr3:42696964-42696981 chr3:42696965-42696981
12	TCF12	chr3:42696049-42697596	ECC-1	luminal epithelium:	n/a	chr3:42697092-42697099
13	POLR2A	chr3:42696682-42697371	U87	brain:	n/a	n/a
14	ESR1	chr3:42696934-42697324	ECC-1	luminal epithelium:	n/a	chr3:42697070-42697085
15	MXI1	chr3:42692903-42697530	SK-N-SH	brain:	n/a	chr3:42696527-42696536 chr3:42696527-42696536 chr3:42694036-42694045 chr3:42696529-42696538
16	EP300	chr3:42696688-42697475	ECC-1	luminal epithelium:	n/a	n/a
17	MXI1	chr3:42692869-42697394	IMR90	lung:	n/a	chr3:42696527-42696536 chr3:42696527-42696536 chr3:42694036-42694045 chr3:42696529-42696538
18	CTBP2	chr3:42696182-42698042	H1-hESC	embryonic stem cell:	n/a	n/a
19	NFIC	chr3:42696084-42697480	ECC-1	luminal epithelium:	n/a	chr3:42696964-42696981 chr3:42696965-42696981

No.	Distal block	Cell Line	Cell type
1	chr3:42695894..42698650-chr3:42786338..42788734,2	K562	blood:
2	chr3:42696300..42698185-chr3:42764015..42766530,4	K562	blood:
3	chr3:42620456..42625490-chr3:42691753..42697487,7	K562	blood:
4	chr3:42629929..42632831-chr3:42695818..42698742,2	MCF-7	breast:
5	chr3:42696300..42697951-chr3:42764752..42766530,2	K562	blood:

Variant related genes	Relation type
ZBTB47	TF binding region
ENSG00000230084	TF binding region
ENSG00000008324	Chromatin interaction
ENSG00000093183	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs2136012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271185	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271186	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2976533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs339658	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs339723	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs339725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339727	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs339728	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339733	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342507	0.81[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs342508	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs342521	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342522	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342536	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342537	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3774398	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4549	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs586082	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs587712	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs597498	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs607568	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs612733	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs614323	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs617722	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs627664	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs638836	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs639692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs640689	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441892	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs663673	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs704979	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8351	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs925457	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9865109	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1818302	chr3:42688867-42709062	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv876731	chr3:42690285-42711655	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs339726	NKTR	Cis_1M	lymphoblastoid	RTeQTL
rs339726	TMEM42	cis	cerebellum	SCAN
rs339726	FAM198A	cis	cerebellum	SCAN
rs339726	NKTR	cis	Nerve Tibial	GTEx
rs339726	NKTR	cis	parietal	SCAN
rs339726	SEC22C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42696200-42697400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:42696200-42697400	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr3:42696200-42697400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr3:42696200-42697600	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr3:42696200-42698400	Enhancers	Fetal Brain Male	brain
6	chr3:42696400-42697400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:42696400-42697400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:42696400-42697400	Enhancers	Fetal Heart	heart
9	chr3:42696400-42697400	Flanking Active TSS	HepG2	liver
10	chr3:42696400-42697400	Flanking Active TSS	NH-A	brain
11	chr3:42696400-42697400	Flanking Active TSS	Osteobl	bone
12	chr3:42696400-42697800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:42696400-42698000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:42696600-42697400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:42696600-42697400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:42696600-42697400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:42696600-42697400	Flanking Active TSS	Brain Substantia Nigra	brain
18	chr3:42696600-42697400	Flanking Active TSS	Colon Smooth Muscle	Colon
19	chr3:42696600-42697400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr3:42696600-42697400	Flanking Active TSS	Right Ventricle	heart
21	chr3:42696600-42697400	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr3:42696600-42697400	Flanking Active TSS	HSMM	muscle
23	chr3:42696600-42697600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:42696600-42697600	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr3:42696600-42697600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr3:42696600-42697600	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr3:42696600-42697600	Flanking Active TSS	NHLF	lung
28	chr3:42696600-42697800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:42696600-42697800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:42696600-42698000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:42696800-42697400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr3:42696800-42697400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr3:42696800-42697400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:42696800-42697400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr3:42696800-42697400	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr3:42696800-42697400	Enhancers	Duodenum Mucosa	Duodenum
37	chr3:42696800-42697600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:42696800-42697600	Flanking Active TSS	Brain Angular Gyrus	brain
39	chr3:42696800-42697600	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr3:42696800-42697800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:42696800-42698000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:42696800-42698000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr3:42696800-42698000	Enhancers	Fetal Intestine Large	intestine
44	chr3:42696800-42698200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:42696800-42698400	Enhancers	Lung	lung
46	chr3:42696800-42698600	Enhancers	Spleen	Spleen
47	chr3:42696800-42701200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:42697000-42697400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:42697000-42697400	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr3:42697000-42697400	Active TSS	Brain Germinal Matrix	brain

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