Variant report

Variant	rs9548865
Chromosome Location	chr13:40229368-40229369
allele	A/G
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	chr13:40229274-40230338	GM19099	blood:	n/a	n/a
2	IRF1	chr13:40229320-40229965	K562	blood:	n/a	chr13:40229682-40229696
3	POLR2A	chr13:40229270-40230395	GM12878	blood:	n/a	n/a
4	POLR2A	chr13:40229131-40230230	GM12891	blood:	n/a	n/a
5	REST	chr13:40229287-40230563	H1-neurons	neurons:	n/a	chr13:40230094-40230107 chr13:40230158-40230171
6	POLR2A	chr13:40229336-40230037	K562	blood:	n/a	n/a
7	POLR2A	chr13:40229260-40229998	MCF10A-Er-Src	breast:	n/a	n/a
8	TBL1XR1	chr13:40229314-40229603	GM12878	blood:	n/a	n/a
9	E2F6	chr13:40229152-40229516	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr13:40229339-40230510	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr13:40229328-40230343	GM15510	blood:	n/a	n/a
12	CUX1	chr13:40229364-40229609	GM12878	blood:	n/a	n/a
13	POLR2A	chr13:40229281-40229997	MCF10A-Er-Src	breast:	n/a	n/a
14	PML	chr13:40229351-40230111	GM12878	blood:	n/a	n/a
15	POLR2A	chr13:40229269-40230202	GM12878	blood:	n/a	n/a
16	POLR2A	chr13:40229245-40230434	NB4	blood:	n/a	n/a
17	STAT3	chr13:40229267-40229723	GM12878	blood:	n/a	n/a
18	MYBL2	chr13:40229360-40230031	HepG2	liver:	n/a	n/a
19	ELK1	chr13:40229221-40230070	GM12878	blood:	n/a	n/a
20	RFX5	chr13:40229206-40230015	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr13:40229350-40230262	GM12878	blood:	n/a	n/a
22	JUND	chr13:40229338-40230016	K562	blood:	n/a	chr13:40229687-40229696
23	MXI1	chr13:40229121-40230974	SK-N-SH	brain:	n/a	n/a
24	BHLHE40	chr13:40229262-40229981	GM12878	blood:	n/a	n/a
25	BRCA1	chr13:40229280-40229830	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr13:40229066-40230228	Raji	blood:	n/a	n/a
27	POLR2A	chr13:40229182-40230146	PBDE	blood:	n/a	n/a
28	POLR2A	chr13:40229303-40230176	U87	brain:	n/a	n/a
29	HCFC1	chr13:40229287-40230690	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr13:40229309-40230172	U87	brain:	n/a	n/a
31	MAX	chr13:40229363-40230670	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40224809..40226726-chr13:40227987..40229515,2	K562	blood:
2	chr13:40229027..40231888-chr13:40233465..40236904,4	MCF-7	breast:

Variant related genes	Relation type
COG6	TF binding region
ENSG00000133103	Chromatin interaction
ENSG00000216014	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs3812882	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];0.98[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3812887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3812888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4142370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4278626	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4312180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4384490	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4415900	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4941936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4941937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4941938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4941939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4941941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4943686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943691	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6563732	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67976778	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7325068	0.85[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap]
rs7325655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs7327779	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7332791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7334651	0.91[JPT][hapmap]
rs7335799	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7984113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs7984958	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9315720	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9315725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9532408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9532410	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9532411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9532412	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9532413	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9532414	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9532420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9548859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9548862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9548863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9548866	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548868	0.94[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];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548869	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548870	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548893	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9548894	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9548896	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9548901	0.81[JPT][hapmap]
rs9548930	0.84[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap]
rs9566471	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9566472	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9576874	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576875	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576881	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9576882	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];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9548865	COG6	Cis_1M	lymphoblastoid	RTeQTL
rs9548865	COG6	cis	Muscle Skeletal	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40227400-40229400	Weak transcription	Aorta	Aorta
2	chr13:40228800-40229400	Weak transcription	Thymus	Thymus
3	chr13:40229000-40229400	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr13:40229000-40230400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr13:40229200-40229400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr13:40229200-40229400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr13:40229200-40229400	Enhancers	Primary B cells from peripheral blood	blood
8	chr13:40229200-40229400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr13:40229200-40229400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr13:40229200-40229400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr13:40229200-40229400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr13:40229200-40229400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:40229200-40229400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr13:40229200-40229400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr13:40229200-40229400	Enhancers	Brain Angular Gyrus	brain
16	chr13:40229200-40229400	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr13:40229200-40229400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr13:40229200-40229400	Enhancers	Hela-S3	cervix
19	chr13:40229200-40229400	Enhancers	HMEC	breast
20	chr13:40229200-40229400	Enhancers	NHDF-Ad	bronchial
21	chr13:40229200-40229600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr13:40229200-40229600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr13:40229200-40229600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr13:40229200-40229600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr13:40229200-40229600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr13:40229200-40229600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr13:40229200-40229600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr13:40229200-40229600	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr13:40229200-40229600	Flanking Active TSS	Brain Cingulate Gyrus	brain
30	chr13:40229200-40229600	Flanking Active TSS	Fetal Brain Male	brain
31	chr13:40229200-40229600	Flanking Active TSS	Fetal Lung	lung
32	chr13:40229200-40229600	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr13:40229200-40229600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr13:40229200-40229600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr13:40229200-40229600	Flanking Active TSS	GM12878-XiMat	blood
36	chr13:40229200-40229600	Flanking Active TSS	HepG2	liver
37	chr13:40229200-40229600	Flanking Active TSS	K562	blood
38	chr13:40229200-40229600	Flanking Active TSS	NHEK	skin
39	chr13:40229200-40229600	Flanking Active TSS	NHLF	lung
40	chr13:40229200-40229600	Flanking Active TSS	Osteobl	bone
41	chr13:40229200-40229800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr13:40229200-40229800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr13:40229200-40229800	Flanking Active TSS	Dnd41	blood
44	chr13:40229200-40229800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr13:40229200-40230200	Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr13:40229200-40230400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr13:40229200-40230400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr13:40229200-40230400	Active TSS	Liver	Liver
49	chr13:40229200-40230400	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr13:40229200-40230400	Active TSS	HSMM	muscle

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