Variant report

Variant	rs3812846
Chromosome Location	chr13:76123298-76123299
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	TCF12	chr13:76123269-76124131	ECC-1	luminal epithelium:	n/a	chr13:76123580-76123587
2	MAX	chr13:76123221-76124773	HCT-116	colon:	n/a	chr13:76123388-76123398 chr13:76123593-76123600 chr13:76123590-76123600
3	RAD21	chr13:76123267-76123841	A549	lung:	n/a	n/a
4	RAD21	chr13:76123260-76123727	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr13:76123155-76124625	PBDE	blood:	n/a	n/a
6	POLR2A	chr13:76123257-76124392	IMR90	lung:	n/a	n/a
7	ELF1	chr13:76123263-76124104	GM12878	blood:	n/a	chr13:76123940-76123952
8	PAX5	chr13:76123198-76123730	GM12878	blood:	n/a	n/a
9	CHD1	chr13:76122548-76124962	IMR90	lung:	n/a	n/a
10	MAX	chr13:76123189-76124235	MCF-7	breast:	n/a	chr13:76123388-76123398 chr13:76123593-76123600 chr13:76123590-76123600
11	POLR2A	chr13:76123286-76124239	A549	lung:	n/a	n/a
12	KAP1	chr13:76123134-76124676	HEK293	kidney:	n/a	n/a
13	MAX	chr13:76123164-76124237	A549	lung:	n/a	chr13:76123388-76123398 chr13:76123593-76123600 chr13:76123590-76123600
14	POLR2A	chr13:76123155-76124278	GM12878	blood:	n/a	n/a
15	RAD21	chr13:76123246-76124069	IMR90	lung:	n/a	n/a
16	CTCF	chr13:76123292-76123670	A549	lung:	n/a	n/a
17	MYC	chr13:76123121-76124399	A549	lung:	n/a	chr13:76123388-76123398 chr13:76123593-76123600 chr13:76123590-76123600
18	SIN3AK20	chr13:76123257-76124713	K562	blood:	n/a	n/a
19	JUND	chr13:76122952-76124844	SK-N-SH	brain:	n/a	chr13:76124478-76124489 chr13:76124728-76124737
20	RAD21	chr13:76123228-76123852	MCF-7	breast:	n/a	n/a
21	KAP1	chr13:76123283-76125049	U2OS	brain:	n/a	n/a
22	POLR2A	chr13:76123298-76124235	ECC-1	luminal epithelium:	n/a	n/a
23	CHD1	chr13:76123286-76124375	GM12878	blood:	n/a	n/a
24	RAD21	chr13:76123200-76123765	H1-hESC	embryonic stem cell:	n/a	n/a
25	MBD4	chr13:76123271-76123766	HepG2	liver:	n/a	n/a
26	ATF2	chr13:76123176-76123915	GM12878	blood:	n/a	n/a
27	ZEB1	chr13:76123293-76123685	GM12878	blood:	n/a	n/a
28	CTCF	chr13:76123277-76123703	T-47D	breast:	n/a	n/a
29	CTCF	chr13:76123254-76123701	K562	blood:	n/a	n/a
30	RAD21	chr13:76123239-76123851	GM12878	blood:	n/a	n/a
31	RAD21	chr13:76123286-76123999	SK-N-SH_RA	brain:	n/a	n/a
32	CTCF	chr13:76123238-76123916	HCT-116	colon:	n/a	n/a
33	HEY1	chr13:76123268-76124238	HepG2	liver:	n/a	n/a
34	NRF1	chr13:76123136-76123906	GM12878	blood:	n/a	chr13:76123615-76123626
35	SMC3	chr13:76123205-76123916	HepG2	liver:	n/a	n/a
36	MYC	chr13:76123290-76123907	H1-hESC	embryonic stem cell:	n/a	chr13:76123388-76123398 chr13:76123593-76123600 chr13:76123590-76123600
37	POLR2A	chr13:76123197-76124417	PFSK-1	brain:	n/a	n/a
38	GTF2F1	chr13:76123284-76123660	H1-hESC	embryonic stem cell:	n/a	n/a
39	RAD21	chr13:76123176-76124345	HCT-116	colon:	n/a	chr13:76124293-76124303 chr13:76124291-76124303
40	MAFK	chr13:76123292-76123697	HepG2	liver:	n/a	n/a
41	RCOR1	chr13:76122686-76123679	K562	blood:	n/a	n/a
42	RAD21	chr13:76123269-76123738	HepG2	liver:	n/a	n/a
43	BCLAF1	chr13:76123288-76124229	GM12878	blood:	n/a	n/a
44	EP300	chr13:76123251-76124607	GM12878	blood:	n/a	chr13:76124094-76124108
45	CTCF	chr13:76122734-76124088	A549	lung:	n/a	n/a
46	CTCF	chr13:76123200-76123671	HepG2	liver:	n/a	n/a
47	MAX	chr13:76123221-76124424	H1-hESC	embryonic stem cell:	n/a	chr13:76123388-76123398 chr13:76123593-76123600 chr13:76123590-76123600
48	CTCF	chr13:76123257-76123685	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr13:76123289-76124573	Hela-S3	cervix:	n/a	n/a
50	ELK1	chr13:76123186-76124610	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:76056169..76056921-chr13:76123095..76123971,5	MCF-7	breast:
2	chr13:76111452..76114150-chr13:76122087..76125338,6	MCF-7	breast:
3	chr13:76055137..76056712-chr13:76122225..76124650,2	MCF-7	breast:
4	chr13:76055434..76058277-chr13:76123047..76126766,3	K562	blood:
5	chr13:76109717..76113590-chr13:76122029..76126081,5	MCF-7	breast:

Variant related genes	Relation type
UCHL3	TF binding region
ENSG00000261553	TF binding region
ENSG00000136111	Chromatin interaction
ENSG00000188243	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11840945	0.86[ASN][1000 genomes]
rs12866456	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12872149	0.86[ASN][1000 genomes]
rs1323696	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs1535726	0.83[ASN][1000 genomes]
rs2031235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2274049	0.83[ASN][1000 genomes]
rs2281762	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2328961	1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2328962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3812844	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3812845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[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]
rs4539477	0.81[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap]
rs4884008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4885312	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4885313	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4885314	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4885319	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs4885321	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs4885328	0.83[ASN][1000 genomes]
rs4885330	0.82[ASN][1000 genomes]
rs4885331	0.82[ASN][1000 genomes]
rs4885332	0.82[ASN][1000 genomes]
rs4885333	0.82[ASN][1000 genomes]
rs61960594	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6562912	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6562920	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7139862	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7317893	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7319334	0.83[CHB][hapmap]
rs7319441	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7326807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7331205	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7358977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7982534	0.99[ASN][1000 genomes]
rs7982613	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs7984443	1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs7995040	0.84[CHB][hapmap]
rs7995889	0.95[ASN][1000 genomes]
rs8000062	1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs8192738	1.00[ASN][1000 genomes]
rs8192741	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8192746	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs8192747	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8192748	0.81[CHB][hapmap];0.82[JPT][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8192751	0.90[ASN][1000 genomes]
rs8192753	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs9318357	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9318358	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9530450	0.83[ASN][1000 genomes]
rs9530453	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap]
rs9530456	0.81[ASN][1000 genomes]
rs9543969	0.81[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][hapmap]
rs9543976	0.87[YRI][hapmap]
rs9543980	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9543994	1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs9543996	0.86[ASN][1000 genomes]
rs9543997	0.86[ASN][1000 genomes]
rs9543999	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9544008	0.83[ASN][1000 genomes]
rs9565175	0.90[ASN][1000 genomes]
rs9573580	0.81[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][hapmap]
rs9573584	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9573590	0.85[ASN][1000 genomes]
rs9635000	0.85[ASN][1000 genomes]
rs966058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs966059	0.81[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs972542	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs975938	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761803	chr13:75943309-76161774	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv900562	chr13:76072743-76176680	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900563	chr13:76093935-76169347	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv900564	chr13:76100090-76156136	Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv900565	chr13:76111280-76169347	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3812846	COMMD6	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76112600-76123600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:76122000-76123600	Flanking Active TSS	Dnd41	blood
3	chr13:76122800-76123400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr13:76122800-76123400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr13:76122800-76123400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
6	chr13:76122800-76123400	Flanking Active TSS	HepG2	liver
7	chr13:76122800-76123800	Flanking Active TSS	Osteobl	bone
8	chr13:76122800-76124800	Active TSS	Brain Anterior Caudate	brain
9	chr13:76122800-76124800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr13:76122800-76124800	Active TSS	A549	lung
11	chr13:76123000-76123400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
12	chr13:76123000-76123400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr13:76123000-76123400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr13:76123000-76123400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr13:76123000-76123400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr13:76123000-76123400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr13:76123000-76123400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr13:76123000-76123400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr13:76123000-76123400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr13:76123000-76123400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr13:76123000-76123400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr13:76123000-76123400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr13:76123000-76123400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr13:76123000-76123400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
25	chr13:76123000-76123400	Flanking Active TSS	Fetal Brain Male	brain
26	chr13:76123000-76123400	Flanking Active TSS	Fetal Brain Female	brain
27	chr13:76123000-76123400	Flanking Active TSS	Fetal Kidney	kidney
28	chr13:76123000-76123400	Flanking Active TSS	GM12878-XiMat	blood
29	chr13:76123000-76123400	Flanking Active TSS	HSMM	muscle
30	chr13:76123000-76123400	Flanking Active TSS	K562	blood
31	chr13:76123000-76123400	Flanking Active TSS	NHDF-Ad	bronchial
32	chr13:76123000-76123400	Flanking Active TSS	NHEK	skin
33	chr13:76123000-76123600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr13:76123000-76123600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr13:76123000-76123600	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr13:76123000-76123600	Enhancers	Primary B cells from peripheral blood	blood
37	chr13:76123000-76123600	Enhancers	Primary T cells fromperipheralblood	blood
38	chr13:76123000-76123600	Enhancers	Primary hematopoietic stem cells	blood
39	chr13:76123000-76123600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr13:76123000-76123600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr13:76123000-76123600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr13:76123000-76123600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr13:76123000-76123600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr13:76123000-76124400	Active TSS	Brain Cingulate Gyrus	brain
45	chr13:76123000-76124400	Active TSS	Brain Substantia Nigra	brain
46	chr13:76123000-76124400	Active TSS	Fetal Muscle Leg	muscle
47	chr13:76123000-76124600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr13:76123000-76124600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr13:76123000-76124600	Active TSS	Colonic Mucosa	Colon
50	chr13:76123000-76124600	Active TSS	Rectal Smooth Muscle	rectum

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