Variant report

Variant	rs3759545
Chromosome Location	chr14:39582888-39582889
allele	G/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	HCFC1	chr14:39582267-39584355	Hela-S3	cervix:	n/a	n/a
2	NRF1	chr14:39582789-39583696	Hela-S3	cervix:	n/a	chr14:39583477-39583491 chr14:39583504-39583515 chr14:39583480-39583491 chr14:39583480-39583494
3	STAT3	chr14:39582483-39582931	MCF10A-Er-Src	breast:	n/a	chr14:39582859-39582870
4	TBL1XR1	chr14:39582882-39584161	K562	blood:	n/a	n/a
5	MTA3	chr14:39582882-39584655	GM12878	blood:	n/a	n/a
6	TBP	chr14:39582857-39583982	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:39580731..39583379-chr14:39639659..39641422,2	K562	blood:
2	chr14:39582528..39584759-chr14:39643385..39645029,2	K562	blood:
3	chr14:39576571..39578731-chr14:39581364..39582921,2	MCF-7	breast:
4	chr14:39582116..39585012-chr14:39643452..39645860,4	MCF-7	breast:
5	chr14:39582047..39584964-chr14:39643383..39645099,4	K562	blood:
6	chr14:39582622..39586619-chr14:39638047..39642701,6	MCF-7	breast:
7	chr14:39581660..39583614-chr5:118323067..118325473,2	MCF-7	breast:

Variant related genes	Relation type
GEMIN2	TF binding region
SEC23A	TF binding region
ENSG00000182400	Chromatin interaction
ENSG00000259083	Chromatin interaction
ENSG00000169570	Chromatin interaction
ENSG00000258591	Chromatin interaction
ENSG00000100941	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10130972	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10133797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10136536	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10140341	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10149120	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10151683	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1061583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11157041	0.86[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.82[MKK][hapmap]
rs12147991	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12437405	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12883061	0.82[EUR][1000 genomes]
rs12885242	0.86[CHB][hapmap];0.93[GIH][hapmap]
rs12891258	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12894046	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13379360	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17108846	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2415524	0.83[AMR][1000 genomes]
rs2737721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2737729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2753606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28379470	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28485301	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28502115	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2869	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28810420	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28856917	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34642409	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34816815	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35035794	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35224434	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35423721	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35992529	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3742354	0.93[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4143954	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902405	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902406	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902418	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902431	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902435	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs532	0.81[CEU][hapmap]
rs58851254	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6571893	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67248626	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71407780	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7147194	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7153124	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8006879	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8009933	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs9322992	0.86[CHB][hapmap]
rs9322994	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3759545	TRAPPC6B	cis	multi-tissue	Pritchard
rs3759545	SSTR1	cis	parietal	SCAN
rs3759545	SIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39573400-39583000	Weak transcription	HSMM	muscle
2	chr14:39573800-39583000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr14:39573800-39583000	Weak transcription	Thymus	Thymus
4	chr14:39574000-39583000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr14:39574000-39583000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr14:39574000-39583000	Weak transcription	Stomach Mucosa	stomach
7	chr14:39574200-39583000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr14:39579600-39583000	Weak transcription	K562	blood
9	chr14:39579800-39583000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr14:39579800-39583000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr14:39580000-39583400	Weak transcription	Gastric	stomach
12	chr14:39581800-39584200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr14:39582200-39583000	Weak transcription	Fetal Intestine Small	intestine
14	chr14:39582400-39583000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr14:39582400-39583000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr14:39582400-39583000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr14:39582400-39583000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr14:39582400-39583000	Enhancers	Hela-S3	cervix
19	chr14:39582400-39583200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr14:39582400-39584200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr14:39582400-39584400	Active TSS	H1 Cell Line	embryonic stem cell
22	chr14:39582400-39584400	Active TSS	A549	lung
23	chr14:39582400-39584600	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr14:39582600-39583000	Enhancers	Brain Anterior Caudate	brain
25	chr14:39582600-39583200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr14:39582600-39583200	Flanking Active TSS	Dnd41	blood
27	chr14:39582800-39583000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr14:39582800-39583000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr14:39582800-39583000	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr14:39582800-39583000	Enhancers	Primary hematopoietic stem cells	blood
31	chr14:39582800-39583000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr14:39582800-39583000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr14:39582800-39583000	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr14:39582800-39583000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr14:39582800-39583000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr14:39582800-39583000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr14:39582800-39583000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr14:39582800-39583000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr14:39582800-39583000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr14:39582800-39583000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr14:39582800-39583000	Enhancers	Adipose Nuclei	Adipose
42	chr14:39582800-39583000	Enhancers	Liver	Liver
43	chr14:39582800-39583000	Enhancers	Brain Angular Gyrus	brain
44	chr14:39582800-39583000	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr14:39582800-39583000	Enhancers	Fetal Lung	lung
46	chr14:39582800-39583000	Enhancers	Fetal Thymus	thymus
47	chr14:39582800-39583000	Flanking Active TSS	HepG2	liver
48	chr14:39582800-39583000	Enhancers	HUVEC	blood vessel
49	chr14:39582800-39583000	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr14:39582800-39583000	Enhancers	NH-A	brain

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