Variant report

Variant	rs9548867
Chromosome Location	chr13:40229568-40229569
allele	A/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	chr13:40229402-40230537	HepG2	liver:	n/a	n/a
2	POLR2A	chr13:40229530-40230321	GM19193	blood:	n/a	n/a
3	POLR2A	chr13:40229274-40230338	GM19099	blood:	n/a	n/a
4	TBP	chr13:40229374-40229943	Hela-S3	cervix:	n/a	n/a
5	ZEB1	chr13:40229530-40230226	GM12878	blood:	n/a	n/a
6	TAF1	chr13:40229514-40230300	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr13:40229488-40230343	MCF-7	breast:	n/a	n/a
8	POLR2A	chr13:40229515-40230077	GM12892	blood:	n/a	n/a
9	POLR2A	chr13:40229562-40230083	HepG2	liver:	n/a	n/a
10	MXI1	chr13:40229461-40229988	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr13:40229531-40230066	HepG2	liver:	n/a	n/a
12	IRF1	chr13:40229320-40229965	K562	blood:	n/a	chr13:40229682-40229696
13	POLR2A	chr13:40229270-40230395	GM12878	blood:	n/a	n/a
14	POLR2A	chr13:40229131-40230230	GM12891	blood:	n/a	n/a
15	TCF12	chr13:40229567-40230197	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr13:40229497-40230081	HepG2	liver:	n/a	n/a
17	POLR2A	chr13:40229403-40230041	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr13:40229543-40230138	GM12892	blood:	n/a	n/a
19	MAX	chr13:40229516-40230059	Hela-S3	cervix:	n/a	n/a
20	E2F6	chr13:40229564-40230206	K562	blood:	n/a	chr13:40229683-40229695
21	MAX	chr13:40229479-40230075	ECC-1	luminal epithelium:	n/a	n/a
22	SIN3A	chr13:40229513-40230058	GM12878	blood:	n/a	n/a
23	ZBTB7A	chr13:40229371-40230174	ECC-1	luminal epithelium:	n/a	n/a
24	MTA3	chr13:40229401-40230197	GM12878	blood:	n/a	n/a
25	REST	chr13:40229287-40230563	H1-neurons	neurons:	n/a	chr13:40230094-40230107 chr13:40230158-40230171
26	POLR2A	chr13:40229548-40230083	HEK293	kidney:	n/a	n/a
27	MYC	chr13:40229547-40230698	NB4	blood:	n/a	n/a
28	MAX	chr13:40229441-40230097	A549	lung:	n/a	n/a
29	POLR2A	chr13:40229393-40230130	HUVEC	blood vessel:	n/a	n/a
30	MAX	chr13:40229543-40230128	H1-hESC	embryonic stem cell:	n/a	n/a
31	NRF1	chr13:40229370-40229987	GM12878	blood:	n/a	chr13:40229784-40229795 chr13:40229765-40229776
32	RCOR1	chr13:40229429-40229961	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr13:40229443-40230090	U87	brain:	n/a	n/a
34	ELF1	chr13:40229548-40229955	K562	blood:	n/a	chr13:40229751-40229762 chr13:40229750-40229763 chr13:40229752-40229761
35	CHD2	chr13:40229544-40230501	GM12878	blood:	n/a	n/a
36	RFX5	chr13:40229554-40230007	GM12878	blood:	n/a	n/a
37	POLR2A	chr13:40229524-40230149	K562	blood:	n/a	n/a
38	POLR2A	chr13:40229536-40230063	HCT-116	colon:	n/a	n/a
39	POLR2A	chr13:40229336-40230037	K562	blood:	n/a	n/a
40	POLR2A	chr13:40229260-40229998	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr13:40229461-40230179	GM12892	blood:	n/a	n/a
42	TAF1	chr13:40229502-40230117	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr13:40229530-40230012	ECC-1	luminal epithelium:	n/a	n/a
44	TBL1XR1	chr13:40229314-40229603	GM12878	blood:	n/a	n/a
45	ZBTB7A	chr13:40229538-40230302	ECC-1	luminal epithelium:	n/a	n/a
46	TAF1	chr13:40229566-40230224	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr13:40229535-40230072	K562	blood:	n/a	n/a
48	GABPA	chr13:40229539-40230124	MCF-7	breast:	n/a	n/a
49	POLR2A	chr13:40229550-40230100	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr13:40229491-40230319	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40229027..40231888-chr13:40233465..40236904,4	MCF-7	breast:

Variant related genes	Relation type
COG6	TF binding region
ENSG00000133103	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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[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];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3812888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4312180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4384490	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4415900	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4941939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4941941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.90[AMR][1000 genomes];0.91[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];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943687	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943691	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6563732	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67976778	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7325068	0.91[JPT][hapmap]
rs7325655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs7327779	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7332791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[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[JPT][hapmap]
rs7984958	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[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];0.90[AMR][1000 genomes];0.91[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	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9532412	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9532413	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9532414	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9532420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[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]
rs9548865	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]
rs9548866	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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548870	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548893	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9548894	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9548896	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9548901	0.83[JPT][hapmap]
rs9548930	0.81[JPT][hapmap]
rs9566471	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9566472	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9576874	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576875	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576881	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];0.99[ASN][1000 genomes]
rs9576882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[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
rs9548867	COG6	cis	Muscle Skeletal	GTEx
rs9548867	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40229000-40230400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr13:40229200-40229600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr13:40229200-40229600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:40229200-40229600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr13:40229200-40229600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
6	chr13:40229200-40229600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr13:40229200-40229600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
8	chr13:40229200-40229600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr13:40229200-40229600	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr13:40229200-40229600	Flanking Active TSS	Brain Cingulate Gyrus	brain
11	chr13:40229200-40229600	Flanking Active TSS	Fetal Brain Male	brain
12	chr13:40229200-40229600	Flanking Active TSS	Fetal Lung	lung
13	chr13:40229200-40229600	Flanking Active TSS	Rectal Smooth Muscle	rectum
14	chr13:40229200-40229600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr13:40229200-40229600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr13:40229200-40229600	Flanking Active TSS	GM12878-XiMat	blood
17	chr13:40229200-40229600	Flanking Active TSS	HepG2	liver
18	chr13:40229200-40229600	Flanking Active TSS	K562	blood
19	chr13:40229200-40229600	Flanking Active TSS	NHEK	skin
20	chr13:40229200-40229600	Flanking Active TSS	NHLF	lung
21	chr13:40229200-40229600	Flanking Active TSS	Osteobl	bone
22	chr13:40229200-40229800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr13:40229200-40229800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr13:40229200-40229800	Flanking Active TSS	Dnd41	blood
25	chr13:40229200-40229800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr13:40229200-40230200	Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr13:40229200-40230400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:40229200-40230400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr13:40229200-40230400	Active TSS	Liver	Liver
30	chr13:40229200-40230400	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr13:40229200-40230400	Active TSS	HSMM	muscle
32	chr13:40229200-40230600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr13:40229200-40230600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr13:40229200-40230600	Active TSS	Brain Hippocampus Middle	brain
35	chr13:40229200-40230600	Active TSS	Brain Substantia Nigra	brain
36	chr13:40229200-40230600	Active TSS	Colon Smooth Muscle	Colon
37	chr13:40229200-40230600	Active TSS	Fetal Heart	heart
38	chr13:40229200-40230800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr13:40229200-40230800	Active TSS	Brain Anterior Caudate	brain
40	chr13:40229200-40230800	Active TSS	Psoas Muscle	Psoas
41	chr13:40229200-40230800	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr13:40229200-40230800	Active TSS	Right Atrium	heart
43	chr13:40229200-40230800	Active TSS	Right Ventricle	heart
44	chr13:40229200-40231000	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr13:40229200-40231000	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr13:40229200-40231000	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr13:40229200-40231000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr13:40229200-40231000	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr13:40229200-40231000	Active TSS	Stomach Smooth Muscle	stomach
50	chr13:40229200-40231000	Active TSS	A549	lung

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