Variant report

Variant	rs3812844
Chromosome Location	chr13:76123456-76123457
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	EGR1	chr13:76123429-76124076	K562	blood:	n/a	n/a
3	NFIC	chr13:76123331-76123931	HepG2	liver:	n/a	n/a
4	MXI1	chr13:76123358-76124731	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr13:76123304-76124192	H1-neurons	neurons:	n/a	n/a
6	MAX	chr13:76123221-76124773	HCT-116	colon:	n/a	chr13:76123388-76123398 chr13:76123593-76123600 chr13:76123590-76123600
7	NRF1	chr13:76123375-76123804	K562	blood:	n/a	chr13:76123615-76123626
8	POLR2A	chr13:76123350-76124219	GM12892	blood:	n/a	n/a
9	RFX5	chr13:76123331-76124002	HepG2	liver:	n/a	n/a
10	RAD21	chr13:76123267-76123841	A549	lung:	n/a	n/a
11	NFYA	chr13:76123374-76123715	Hela-S3	cervix:	n/a	n/a
12	CEBPD	chr13:76123400-76123618	HepG2	liver:	n/a	n/a
13	CTCF	chr13:76123440-76123590	HRPEpiC	eye:	n/a	n/a
14	CTCF	chr13:76123420-76123570	HRE	kidney:	n/a	n/a
15	RAD21	chr13:76123260-76123727	ECC-1	luminal epithelium:	n/a	n/a
16	USF1	chr13:76123398-76123671	K562	blood:	n/a	n/a
17	CTCF	chr13:76123440-76123590	GM12864	blood:	n/a	n/a
18	POLR2A	chr13:76123155-76124625	PBDE	blood:	n/a	n/a
19	PML	chr13:76123411-76123859	GM12878	blood:	n/a	n/a
20	CTCF	chr13:76123400-76123550	MCF-7	breast:	n/a	n/a
21	EP300	chr13:76123338-76123896	SK-N-SH_RA	brain:	n/a	n/a
22	CTCF	chr13:76123408-76123677	Medullo	brain:	n/a	n/a
23	TCF3	chr13:76123334-76123647	GM12878	blood:	n/a	n/a
24	POLR2A	chr13:76123257-76124392	IMR90	lung:	n/a	n/a
25	BACH1	chr13:76123391-76124432	H1-hESC	embryonic stem cell:	n/a	n/a
26	ELF1	chr13:76123263-76124104	GM12878	blood:	n/a	chr13:76123940-76123952
27	CTCF	chr13:76123340-76123490	GM12870	blood:	n/a	n/a
28	RCOR1	chr13:76123338-76124727	Hela-S3	cervix:	n/a	n/a
29	PAX5	chr13:76123198-76123730	GM12878	blood:	n/a	n/a
30	CHD1	chr13:76122548-76124962	IMR90	lung:	n/a	n/a
31	MAX	chr13:76123189-76124235	MCF-7	breast:	n/a	chr13:76123388-76123398 chr13:76123593-76123600 chr13:76123590-76123600
32	CTCF	chr13:76123352-76123699	MCF-7	breast:	n/a	n/a
33	POLR2A	chr13:76123286-76124239	A549	lung:	n/a	n/a
34	CTCF	chr13:76123440-76123590	HAc	cerebellar:	n/a	n/a
35	CTCF	chr13:76123440-76123590	HFF	foreskin:	n/a	n/a
36	KAP1	chr13:76123134-76124676	HEK293	kidney:	n/a	n/a
37	EP300	chr13:76123404-76124081	H1-hESC	embryonic stem cell:	n/a	n/a
38	SP4	chr13:76123379-76124006	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAX	chr13:76123164-76124237	A549	lung:	n/a	chr13:76123388-76123398 chr13:76123593-76123600 chr13:76123590-76123600
40	TBP	chr13:76123335-76124146	GM12878	blood:	n/a	n/a
41	TCF12	chr13:76123338-76123672	GM12878	blood:	n/a	chr13:76123580-76123587
42	POLR2A	chr13:76123155-76124278	GM12878	blood:	n/a	n/a
43	TCF7L2	chr13:76123340-76124698	HCT-116	colon:	n/a	n/a
44	RAD21	chr13:76123336-76123703	SK-N-SH_RA	brain:	n/a	n/a
45	MAFK	chr13:76123351-76124588	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr13:76123440-76123590	HepG2	liver:	n/a	n/a
47	RAD21	chr13:76123246-76124069	IMR90	lung:	n/a	n/a
48	CTCF	chr13:76123292-76123670	A549	lung:	n/a	n/a
49	CTCF	chr13:76123440-76123590	HVMF	connective:	n/a	n/a
50	CTCF	chr13:76123440-76123590	HFF-Myc	foreskin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:76111859..76112746-chr13:76123326..76123936,2	MCF-7	breast:
2	chr13:76056169..76056921-chr13:76123095..76123971,5	MCF-7	breast:
3	chr13:76111452..76114150-chr13:76122087..76125338,6	MCF-7	breast:
4	chr13:76055137..76056712-chr13:76122225..76124650,2	MCF-7	breast:
5	chr13:76055434..76058277-chr13:76123047..76126766,3	K562	blood:
6	chr13:76109717..76113590-chr13:76122029..76126081,5	MCF-7	breast:

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

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11840945	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12866456	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs12872149	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1323696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1535726	0.83[ASN][1000 genomes]
rs2031235	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs2274049	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2281762	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];1.00[ASN][1000 genomes]
rs2328961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2328962	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs3812845	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs3812846	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4539477	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4884008	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs4885312	0.90[ASN][1000 genomes]
rs4885313	0.86[ASN][1000 genomes]
rs4885319	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4885321	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4885328	0.83[ASN][1000 genomes]
rs4885330	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4885331	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4885332	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4885333	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61960594	0.83[ASN][1000 genomes]
rs6562920	0.85[ASN][1000 genomes]
rs7139862	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs7319334	0.84[CHB][hapmap]
rs7319441	0.99[ASN][1000 genomes]
rs7326807	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7331205	0.86[ASN][1000 genomes]
rs7358977	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs7491365	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7982534	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7982613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7984443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7995040	0.88[CEU][hapmap];0.84[CHB][hapmap]
rs7995889	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8000062	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8192738	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8192741	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs8192744	1.00[CEU][hapmap]
rs8192746	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8192748	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs8192750	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8192751	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8192753	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9318358	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9530450	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9530453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9530456	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9543969	0.84[CHB][hapmap]
rs9543994	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9543996	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9543997	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9543999	0.83[ASN][1000 genomes]
rs9544008	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9565175	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9573580	0.84[CHB][hapmap]
rs9573584	0.90[ASN][1000 genomes]
rs9573590	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9635000	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs966058	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs966059	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs972542	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs975938	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

No data

Chromatin state (count:124 , 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	chr13:76122800-76123800	Flanking Active TSS	Osteobl	bone
4	chr13:76122800-76124800	Active TSS	Brain Anterior Caudate	brain
5	chr13:76122800-76124800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr13:76122800-76124800	Active TSS	A549	lung
7	chr13:76123000-76123600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr13:76123000-76123600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr13:76123000-76123600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr13:76123000-76123600	Enhancers	Primary B cells from peripheral blood	blood
11	chr13:76123000-76123600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr13:76123000-76123600	Enhancers	Primary hematopoietic stem cells	blood
13	chr13:76123000-76123600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr13:76123000-76123600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr13:76123000-76123600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr13:76123000-76123600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr13:76123000-76123600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr13:76123000-76124400	Active TSS	Brain Cingulate Gyrus	brain
19	chr13:76123000-76124400	Active TSS	Brain Substantia Nigra	brain
20	chr13:76123000-76124400	Active TSS	Fetal Muscle Leg	muscle
21	chr13:76123000-76124600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr13:76123000-76124600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr13:76123000-76124600	Active TSS	Colonic Mucosa	Colon
24	chr13:76123000-76124600	Active TSS	Rectal Smooth Muscle	rectum
25	chr13:76123000-76124800	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr13:76123000-76124800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr13:76123000-76124800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr13:76123000-76124800	Active TSS	Lung	lung
29	chr13:76123000-76124800	Active TSS	Stomach Smooth Muscle	stomach
30	chr13:76123000-76125000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr13:76123000-76125200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr13:76123000-76125600	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr13:76123200-76123600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr13:76123200-76123600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr13:76123200-76123600	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr13:76123200-76123600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr13:76123200-76123600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr13:76123200-76123600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr13:76123200-76123600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr13:76123200-76123600	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr13:76123200-76123600	Flanking Active TSS	Liver	Liver
42	chr13:76123200-76123600	Flanking Active TSS	Fetal Muscle Trunk	muscle
43	chr13:76123200-76123600	Flanking Active TSS	Fetal Thymus	thymus
44	chr13:76123200-76123600	Flanking Active TSS	Pancreas	Pancrea
45	chr13:76123200-76123600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr13:76123200-76123600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr13:76123200-76123600	Flanking Active TSS	HMEC	breast
48	chr13:76123200-76123600	Flanking Active TSS	HUVEC	blood vessel
49	chr13:76123200-76123600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr13:76123200-76124000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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