Variant report

Variant	rs2277113
Chromosome Location	chr6:109775436-109775437
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	FOXM1	chr6:109775435-109776715	GM12878	blood:	n/a	n/a
2	EBF1	chr6:109775184-109775650	GM12878	blood:	n/a	chr6:109775526-109775535 chr6:109775524-109775535 chr6:109775524-109775537 chr6:109775525-109775535 chr6:109775526-109775535
3	CTCF	chr6:109775320-109775470	WI-38	lung:	n/a	n/a
4	EBF1	chr6:109775289-109775711	GM12878	blood:	n/a	chr6:109775526-109775535 chr6:109775524-109775535 chr6:109775524-109775537 chr6:109775525-109775535 chr6:109775526-109775535
5	POLR2A	chr6:109775370-109776972	GM12892	blood:	n/a	n/a
6	POLR2A	chr6:109774791-109778612	GM12892	blood:	n/a	n/a
7	POLR2A	chr6:109775261-109777757	GM19099	blood:	n/a	n/a
8	MTA3	chr6:109774944-109778262	GM12878	blood:	n/a	n/a
9	NRF1	chr6:109775226-109775537	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:109775300-109777378	NB4	blood:	n/a	n/a
11	POLR2A	chr6:109775074-109777912	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:109774855-109777633	GM12892	blood:	n/a	n/a
13	MAX	chr6:109775363-109777255	NB4	blood:	n/a	chr6:109776320-109776330 chr6:109776227-109776237
14	POLR2A	chr6:109775374-109777341	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:109774498-109777592	GM19193	blood:	n/a	n/a
16	STAT5A	chr6:109775299-109776940	GM12878	blood:	n/a	chr6:109776179-109776191 chr6:109776249-109776261
17	POLR2A	chr6:109774247-109777532	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:109775064-109777376	Raji	blood:	n/a	n/a
19	CTCF	chr6:109775247-109775547	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:109774772-109776119	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr6:109775422-109776233	GM12891	blood:	n/a	n/a
22	CHD2	chr6:109775347-109777569	GM12878	blood:	n/a	chr6:109776252-109776262
23	POLR2A	chr6:109774576-109777618	GM18505	blood:	n/a	n/a
24	POLR2A	chr6:109775187-109776209	GM12891	blood:	n/a	n/a
25	POLR2A	chr6:109774967-109777662	GM18951	blood:	n/a	n/a
26	POLR2A	chr6:109774418-109779026	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:109775265-109775440	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:109775024-109779284	GM12891	blood:	n/a	n/a
29	POLR2A	chr6:109774366-109777650	GM12892	blood:	n/a	n/a
30	EBF1	chr6:109775245-109776907	GM12878	blood:	n/a	chr6:109775526-109775535 chr6:109775524-109775535 chr6:109775524-109775537 chr6:109775525-109775535 chr6:109775526-109775535
31	POLR2A	chr6:109774894-109775453	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:109774885-109777969	GM18526	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:109774016..109776250-chr6:109801827..109803875,2	K562	blood:
2	chr6:109742234..109744237-chr6:109774891..109776518,2	MCF-7	breast:
3	chr6:109703058..109705958-chr6:109774873..109777253,2	MCF-7	breast:
4	chr6:109414902..109417715-chr6:109774468..109776378,2	K562	blood:
5	chr6:109702694..109704324-chr6:109775011..109776713,2	K562	blood:

Variant related genes	Relation type
MICAL1	TF binding region
ENSG00000080546	Chromatin interaction
ENSG00000183137	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10457192	0.88[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs10457194	0.87[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs10457195	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs1046943	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1054607	0.82[JPT][hapmap];0.90[YRI][hapmap]
rs1074765	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes]
rs1074766	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10872033	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11153171	0.87[CHB][hapmap]
rs11153183	0.88[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs11251	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11754455	0.87[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs11755641	0.88[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs12194061	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs12197180	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs12198938	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs12199154	0.88[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs12212476	0.87[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs12214147	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12529733	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs13201430	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs13203587	0.82[EUR][1000 genomes]
rs13219952	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13220915	0.87[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs1406899	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs1476387	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1521907	0.88[EUR][1000 genomes]
rs17070591	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17070656	0.85[YRI][hapmap]
rs1885690	0.88[EUR][1000 genomes]
rs1885691	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1980591	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs1998811	0.86[EUR][1000 genomes]
rs2024849	0.82[EUR][1000 genomes]
rs2024850	0.88[CEU][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs2024852	0.82[EUR][1000 genomes]
rs2024853	0.88[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs2211288	0.89[EUR][1000 genomes]
rs2236084	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2277114	0.88[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2884037	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs35146243	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35260632	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3734652	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3757230	0.89[EUR][1000 genomes]
rs3757231	0.89[EUR][1000 genomes]
rs3757235	0.85[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs3778474	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3778478	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3799842	0.96[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3818933	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4636056	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4945831	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4946967	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4946970	0.90[EUR][1000 genomes]
rs4946976	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58644322	0.88[EUR][1000 genomes]
rs59597139	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6568587	0.85[YRI][hapmap]
rs6911838	0.84[CHB][hapmap]
rs6914216	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6920372	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6920712	0.82[JPT][hapmap];0.90[YRI][hapmap]
rs6920962	0.86[YRI][hapmap]
rs6925005	0.85[YRI][hapmap]
rs6939548	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6939953	0.88[EUR][1000 genomes]
rs699700	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs729888	0.88[CEU][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs730089	0.85[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs7356790	0.85[YRI][hapmap]
rs736830	0.85[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs746794	0.89[EUR][1000 genomes]
rs7748669	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7751582	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7754650	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7755941	0.87[CEU][hapmap];0.83[GIH][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs7768973	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7773950	0.88[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs8465	0.88[EUR][1000 genomes]
rs910730	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9320286	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9372213	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs9398202	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9480947	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs9480949	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9480956	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9480958	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9487064	0.82[EUR][1000 genomes]
rs9487066	0.81[EUR][1000 genomes]
rs9487069	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9487070	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs9487076	0.88[EUR][1000 genomes]
rs9487084	0.89[EUR][1000 genomes]
rs9487085	0.88[EUR][1000 genomes]
rs9487103	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs974034	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes]
rs9791241	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2277113	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs2277113	SMPD2	cis	parietal	SCAN
rs2277113	MICAL1	cis	Artery Tibial	GTEx
rs2277113	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs2277113	FIG4	cis	cerebellum	SCAN
rs2277113	FIG4	cis	parietal	SCAN
rs2277113	AKD1	cis	parietal	SCAN
rs2277113	CD164	cis	parietal	SCAN
rs2277113	SMPD2	cis	Esophagus Mucosa	GTEx
rs2277113	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs2277113	AKD1	cis	cerebellum	SCAN
rs2277113	RP11-425D10.10	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109762800-109775800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:109763200-109775600	Weak transcription	Fetal Kidney	kidney
3	chr6:109763200-109775800	Weak transcription	HUVEC	blood vessel
4	chr6:109763600-109775800	Weak transcription	Right Atrium	heart
5	chr6:109763800-109775600	Weak transcription	HepG2	liver
6	chr6:109764400-109775800	Weak transcription	Hela-S3	cervix
7	chr6:109766600-109775800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:109767000-109775600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:109767000-109776000	Weak transcription	A549	lung
10	chr6:109767200-109776000	Weak transcription	Osteobl	bone
11	chr6:109768400-109775800	Weak transcription	Liver	Liver
12	chr6:109768400-109775800	Weak transcription	Left Ventricle	heart
13	chr6:109768400-109776000	Weak transcription	Ovary	ovary
14	chr6:109768400-109776400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:109768400-109776400	Weak transcription	K562	blood
16	chr6:109772000-109775600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:109773200-109775800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:109773400-109775600	Enhancers	Primary hematopoietic stem cells	blood
19	chr6:109773400-109775600	Weak transcription	Aorta	Aorta
20	chr6:109773800-109775600	Enhancers	Fetal Thymus	thymus
21	chr6:109774000-109775600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:109774400-109775600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:109774600-109775600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr6:109774600-109775600	Enhancers	Esophagus	oesophagus
25	chr6:109774600-109775800	Enhancers	Stomach Mucosa	stomach
26	chr6:109774800-109775600	Genic enhancers	Fetal Stomach	stomach
27	chr6:109774800-109775600	Genic enhancers	Right Ventricle	heart
28	chr6:109774800-109775600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
29	chr6:109774800-109775800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:109774800-109775800	Enhancers	Pancreas	Pancrea
31	chr6:109774800-109775800	Enhancers	Small Intestine	intestine
32	chr6:109774800-109776000	Enhancers	Lung	lung
33	chr6:109775000-109775600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:109775000-109775600	Enhancers	Adipose Nuclei	Adipose
35	chr6:109775000-109775600	Enhancers	Brain Hippocampus Middle	brain
36	chr6:109775000-109775600	Enhancers	Fetal Brain Male	brain
37	chr6:109775000-109775800	Weak transcription	NHEK	skin
38	chr6:109775000-109776000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr6:109775000-109776200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr6:109775000-109776200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr6:109775000-109776800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr6:109775000-109776800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:109775200-109775600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:109775200-109775600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:109775200-109775600	Enhancers	Brain Anterior Caudate	brain
46	chr6:109775200-109775600	Enhancers	Brain Substantia Nigra	brain
47	chr6:109775200-109775600	Enhancers	Colon Smooth Muscle	Colon
48	chr6:109775200-109775600	Enhancers	Fetal Lung	lung
49	chr6:109775200-109775600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr6:109775200-109775600	Active TSS	HSMMtube	muscle

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