Variant report

Variant	rs339727
Chromosome Location	chr3:42693126-42693127
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	POLR2A	chr3:42692877-42693718	U87	brain:	n/a	n/a
2	TCF12	chr3:42692708-42694115	ECC-1	luminal epithelium:	n/a	n/a
3	JUND	chr3:42692900-42695764	SK-N-SH	brain:	n/a	chr3:42693498-42693510 chr3:42693230-42693240 chr3:42693230-42693240 chr3:42693230-42693240 chr3:42693229-42693241 chr3:42693500-42693508 chr3:42693230-42693240 chr3:42693499-42693510
4	POLR2A	chr3:42692642-42693314	HepG2	liver:	n/a	n/a
5	FOSL2	chr3:42692958-42694743	SK-N-SH	brain:	n/a	chr3:42693498-42693510 chr3:42693230-42693240 chr3:42693230-42693240 chr3:42693230-42693240 chr3:42693229-42693241 chr3:42693500-42693508 chr3:42693230-42693240 chr3:42693499-42693510
6	POLR2A	chr3:42692960-42693807	U87	brain:	n/a	n/a
7	FOS	chr3:42693124-42693625	MCF10A-Er-Src	breast:	n/a	chr3:42693498-42693510 chr3:42693230-42693240 chr3:42693230-42693240 chr3:42693230-42693240 chr3:42693229-42693241 chr3:42693500-42693508 chr3:42693230-42693240 chr3:42693499-42693510
8	TCF12	chr3:42692854-42695443	SK-N-SH	brain:	n/a	chr3:42694507-42694514 chr3:42694856-42694865
9	NFIC	chr3:42692819-42693812	ECC-1	luminal epithelium:	n/a	n/a
10	PBX3	chr3:42693054-42693801	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr3:42687656-42693228	K562	blood:	n/a	n/a
12	NFIC	chr3:42692871-42693805	ECC-1	luminal epithelium:	n/a	n/a
13	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
14	NFIC	chr3:42692846-42693878	SK-N-SH	brain:	n/a	n/a
15	TEAD4	chr3:42692920-42693765	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr3:42691164-42693454	SK-N-MC	brain:	n/a	n/a
17	TFAP2A	chr3:42693065-42693582	Hela-S3	cervix:	n/a	chr3:42693220-42693232 chr3:42693220-42693232 chr3:42693220-42693232 chr3:42693507-42693518 chr3:42693500-42693509 chr3:42693220-42693232 chr3:42693217-42693232
18	MAX	chr3:42692934-42693707	SK-N-SH	brain:	n/a	chr3:42693401-42693411
19	TEAD4	chr3:42692876-42693730	ECC-1	luminal epithelium:	n/a	n/a
20	FOS	chr3:42693099-42693675	MCF10A-Er-Src	breast:	n/a	chr3:42693498-42693510 chr3:42693230-42693240 chr3:42693230-42693240 chr3:42693230-42693240 chr3:42693229-42693241 chr3:42693500-42693508 chr3:42693230-42693240 chr3:42693499-42693510
21	POLR2A	chr3:42692965-42693750	U87	brain:	n/a	n/a
22	CTCF	chr3:42693020-42693170	HAc	cerebellar:	n/a	n/a
23	TCF7L2	chr3:42692904-42693355	Hela-S3	cervix:	n/a	chr3:42693096-42693105
24	POLR2A	chr3:42692966-42693807	U87	brain:	n/a	n/a
25	E2F4	chr3:42692932-42693141	MCF10A-Er-Src	breast:	n/a	chr3:42693047-42693054 chr3:42693047-42693054 chr3:42693046-42693055 chr3:42693047-42693054 chr3:42693046-42693058
26	MAX	chr3:42692843-42693326	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr3:42693047-42693131	HUVEC	blood vessel:	n/a	n/a
28	EP300	chr3:42692662-42693852	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr3:42693025-42693699	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr3:42690264-42693660	Hela-S3	cervix:	n/a	n/a
31	TCF12	chr3:42692942-42693885	SK-N-SH	brain:	n/a	n/a
32	TCF12	chr3:42692717-42693808	ECC-1	luminal epithelium:	n/a	n/a
33	MXI1	chr3:42692903-42697530	SK-N-SH	brain:	n/a	chr3:42696527-42696536 chr3:42696527-42696536 chr3:42694036-42694045 chr3:42696529-42696538
34	EP300	chr3:42692907-42693655	ECC-1	luminal epithelium:	n/a	n/a
35	MXI1	chr3:42692869-42697394	IMR90	lung:	n/a	chr3:42696527-42696536 chr3:42696527-42696536 chr3:42694036-42694045 chr3:42696529-42696538
36	TFAP2C	chr3:42692968-42693685	Hela-S3	cervix:	n/a	n/a
37	ZNF263	chr3:42693015-42693555	HEK293-T-REx	kidney:	n/a	chr3:42693182-42693203

No.	Distal block	Cell Line	Cell type
1	chr3:42632553..42639930-chr3:42692933..42696882,8	K562	blood:
2	chr3:42655417..42657513-chr3:42690626..42693228,2	K562	blood:
3	chr3:42613871..42615893-chr3:42692209..42694692,2	K562	blood:
4	chr3:42691450..42694328-chr3:42695841..42698236,2	MCF-7	breast:
5	chr3:42620456..42625490-chr3:42691753..42697487,7	K562	blood:
6	chr3:42693104..42694831-chr3:42707360..42709210,2	MCF-7	breast:
7	chr3:42690176..42693159-chr3:42693581..42695274,2	MCF-7	breast:
8	chr3:42688256..42690363-chr3:42691600..42693510,2	MCF-7	breast:
9	chr3:42688509..42691154-chr3:42691239..42693774,3	MCF-7	breast:

Variant related genes	Relation type
ZBTB47	TF binding region
ENSG00000114853	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000230084	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];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271185	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2271186	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2976533	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339658	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339723	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs339725	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs339726	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	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs339733	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342507	0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs342508	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs342521	1.00[CEU][hapmap];0.85[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs342522	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342536	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342537	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3774398	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4549	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs586082	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs587712	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs597498	0.94[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];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs612733	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs614323	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs617722	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs627664	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs638836	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs639692	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs640689	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441892	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs663673	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs689251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs704979	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8351	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs925457	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9865109	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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
rs339727	FAM198A	cis	cerebellum	SCAN
rs339727	NKTR	cis	parietal	SCAN
rs339727	TMEM42	cis	cerebellum	SCAN
rs339727	NKTR	Cis_1M	lymphoblastoid	RTeQTL
rs339727	SEC22C	Cis_1M	lymphoblastoid	RTeQTL
rs339727	NKTR	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42685000-42693600	Weak transcription	Stomach Mucosa	stomach
2	chr3:42686400-42695000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:42686600-42693800	Weak transcription	Colonic Mucosa	Colon
4	chr3:42686600-42694200	Weak transcription	Fetal Brain Male	brain
5	chr3:42686600-42694800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:42686800-42694600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:42687800-42693800	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr3:42688600-42694800	Weak transcription	Fetal Kidney	kidney
9	chr3:42688800-42693400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:42688800-42694800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:42689000-42694400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:42689600-42693200	Weak transcription	Small Intestine	intestine
13	chr3:42689600-42693600	Weak transcription	Pancreas	Pancrea
14	chr3:42690000-42693200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr3:42690000-42693600	Weak transcription	Psoas Muscle	Psoas
16	chr3:42690000-42694200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:42690400-42694200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:42690600-42693200	Enhancers	Brain Substantia Nigra	brain
19	chr3:42690600-42693400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:42690600-42693600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:42690600-42693600	Weak transcription	Fetal Lung	lung
22	chr3:42690600-42693600	Weak transcription	K562	blood
23	chr3:42690600-42693800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr3:42690600-42693800	Weak transcription	GM12878-XiMat	blood
25	chr3:42690600-42694000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:42690600-42694000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:42690600-42694800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:42690800-42693200	Weak transcription	Fetal Heart	heart
29	chr3:42690800-42693800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:42690800-42694400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr3:42691000-42693400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:42691000-42693800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:42691000-42694000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:42691000-42694400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:42691400-42693800	Enhancers	Left Ventricle	heart
36	chr3:42691400-42694600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:42691600-42694800	Enhancers	Placenta Amnion	Placenta Amnion
38	chr3:42691800-42693200	Enhancers	Aorta	Aorta
39	chr3:42691800-42693400	Weak transcription	Fetal Intestine Large	intestine
40	chr3:42691800-42693800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:42691800-42693800	Transcr. at gene 5' and 3'	Brain Anterior Caudate	brain
42	chr3:42691800-42694600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr3:42691800-42695200	Weak transcription	Thymus	Thymus
44	chr3:42692000-42693200	Weak transcription	Spleen	Spleen
45	chr3:42692000-42693800	Weak transcription	Brain Germinal Matrix	brain
46	chr3:42692000-42694600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:42692000-42694800	Weak transcription	Primary T cells from cord blood	blood
48	chr3:42692200-42693200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:42692200-42693200	Weak transcription	Adipose Nuclei	Adipose
50	chr3:42692200-42693400	Weak transcription	Fetal Brain Female	brain

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