Variant report

Variant	rs6785238
Chromosome Location	chr3:53926235-53926236
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	chr3:53925592-53926340	HepG2	liver:	n/a	n/a
2	GABPA	chr3:53925663-53926426	MCF-7	breast:	n/a	n/a
3	POU2F2	chr3:53925373-53926356	GM12878	blood:	n/a	n/a
4	BCLAF1	chr3:53925490-53926439	GM12878	blood:	n/a	chr3:53925670-53925683 chr3:53925669-53925682
5	POLR2A	chr3:53925664-53926255	GM12891	blood:	n/a	n/a
6	GABPA	chr3:53925688-53926253	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:53925563-53926613	U87	brain:	n/a	n/a
8	MAX	chr3:53925506-53926572	A549	lung:	n/a	n/a
9	SRF	chr3:53925475-53926530	HCT-116	colon:	n/a	n/a
10	NFYB	chr3:53925685-53926353	GM12878	blood:	n/a	chr3:53925950-53925964 chr3:53925949-53925964 chr3:53925951-53925966 chr3:53925952-53925962 chr3:53925949-53925964
11	TAF1	chr3:53925106-53926405	H1-hESC	embryonic stem cell:	n/a	n/a
12	FOS	chr3:53925875-53926390	MCF10A-Er-Src	breast:	n/a	n/a
13	GABPA	chr3:53925792-53926252	HepG2	liver:	n/a	n/a
14	PBX3	chr3:53925674-53926453	SK-N-SH	brain:	n/a	chr3:53925952-53925961
15	YY1	chr3:53925565-53926337	H1-hESC	embryonic stem cell:	n/a	chr3:53925673-53925682 chr3:53926023-53926032
16	MAZ	chr3:53925528-53926396	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr3:53925214-53926549	Hela-S3	cervix:	n/a	n/a
18	IRF1	chr3:53925655-53926324	K562	blood:	n/a	chr3:53925953-53925962
19	E2F6	chr3:53925457-53926636	K562	blood:	n/a	n/a
20	POLR2A	chr3:53925215-53926443	GM19099	blood:	n/a	n/a
21	POLR2A	chr3:53925577-53926385	PANC-1	pancreas:	n/a	n/a
22	YY1	chr3:53925538-53926429	SK-N-SH	brain:	n/a	chr3:53925673-53925682 chr3:53926023-53926032
23	POLR2A	chr3:53925993-53926366	HUVEC	blood vessel:	n/a	n/a
24	TAF1	chr3:53925942-53926270	HepG2	liver:	n/a	n/a
25	PML	chr3:53925445-53926480	GM12878	blood:	n/a	n/a
26	CREB1	chr3:53924970-53926510	K562	blood:	n/a	n/a
27	POLR2A	chr3:53925577-53926400	PANC-1	pancreas:	n/a	n/a
28	MAFF	chr3:53925693-53926320	HepG2	liver:	n/a	chr3:53925918-53925936
29	CREB1	chr3:53924997-53926439	GM12878	blood:	n/a	n/a
30	EP300	chr3:53925759-53926312	K562	blood:	n/a	n/a
31	CREB1	chr3:53925732-53926284	A549	lung:	n/a	n/a
32	BCLAF1	chr3:53925463-53926403	GM12878	blood:	n/a	chr3:53925670-53925683 chr3:53925669-53925682
33	SETDB1	chr3:53925733-53926441	U2OS	brain:	n/a	n/a
34	HA-E2F1	chr3:53925654-53926354	MCF-7	breast:	n/a	n/a
35	POLR2A	chr3:53925489-53926467	Gliobla	brain:	n/a	n/a
36	POLR2A	chr3:53925633-53926372	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr3:53923739-53926749	PBDE	blood:	n/a	n/a
38	YY1	chr3:53925450-53926339	HepG2	liver:	n/a	chr3:53925673-53925682 chr3:53926023-53926032
39	TCF12	chr3:53925689-53926438	ECC-1	luminal epithelium:	n/a	n/a
40	YY1	chr3:53925686-53926316	SK-N-SH_RA	brain:	n/a	chr3:53926023-53926032
41	POLR2A	chr3:53925590-53926409	MCF-7	breast:	n/a	n/a
42	WRNIP1	chr3:53924966-53926330	GM12878	blood:	n/a	n/a
43	ZNF143	chr3:53925720-53926246	K562	blood:	n/a	n/a
44	HDAC2	chr3:53925726-53926369	HepG2	liver:	n/a	n/a
45	MAX	chr3:53925706-53926750	H1-hESC	embryonic stem cell:	n/a	n/a
46	USF2	chr3:53925721-53926631	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:53925423-53926425	GM12892	blood:	n/a	n/a
48	PBX3	chr3:53925604-53926533	SK-N-SH	brain:	n/a	chr3:53925952-53925961
49	FOS	chr3:53925871-53926401	MCF10A-Er-Src	breast:	n/a	n/a
50	ZNF143	chr3:53925581-53926325	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:53914775..53921125-chr3:53923203..53927129,12	MCF-7	breast:
2	chr12:13043989..13044920-chr3:53925634..53926622,2	Hela-S3	cervix:
3	chr3:53915297..53916473-chr3:53925441..53926286,3	MCF-7	breast:
4	chr15:72410138..72410841-chr3:53925749..53926410,2	Hela-S3	cervix:
5	chr3:53909521..53911477-chr3:53924349..53927028,2	MCF-7	breast:
6	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
7	chr3:53913820..53918433-chr3:53924406..53927799,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113811	TF binding region
ENSG00000013588	Chromatin interaction
ENSG00000066933	Chromatin interaction
ENSG00000222888	Chromatin interaction
ENSG00000113812	Chromatin interaction
ENSG00000166192	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11130383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11130384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11562	0.83[AFR][1000 genomes]
rs12715465	1.00[AMR][1000 genomes]
rs13321898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13322337	1.00[AMR][1000 genomes]
rs13434145	1.00[AMR][1000 genomes]
rs28409957	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6782007	1.00[AMR][1000 genomes]
rs6802878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72556356	1.00[AMR][1000 genomes]
rs7614233	1.00[AMR][1000 genomes]
rs7636496	1.00[AMR][1000 genomes]
rs7637908	1.00[AMR][1000 genomes]
rs7640840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9814675	1.00[AMR][1000 genomes]
rs9816010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9818571	1.00[AMR][1000 genomes]
rs9823141	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9830672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9833359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9834168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9835258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9849610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9852243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9859937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9860224	1.00[AMR][1000 genomes]
rs9872403	1.00[AMR][1000 genomes]
rs9878250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882134	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1014752	chr3:53912429-54123246	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr3:53923400-53926400	Active TSS	Right Ventricle	heart
2	chr3:53923600-53926600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr3:53924000-53926400	Active TSS	Colonic Mucosa	Colon
4	chr3:53924200-53926600	Active TSS	Psoas Muscle	Psoas
5	chr3:53924200-53926600	Active TSS	Right Atrium	heart
6	chr3:53924200-53926800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:53924400-53926400	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr3:53924400-53926400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:53924400-53926800	Active TSS	HSMMtube	muscle
10	chr3:53924600-53926400	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr3:53924600-53926400	Active TSS	Fetal Intestine Large	intestine
12	chr3:53924600-53926400	Active TSS	GM12878-XiMat	blood
13	chr3:53924600-53926600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr3:53924600-53926800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr3:53924600-53926800	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:53924600-53926800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:53924800-53926400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:53924800-53926400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:53924800-53926400	Active TSS	Aorta	Aorta
20	chr3:53924800-53926400	Active TSS	Lung	lung
21	chr3:53924800-53926400	Active TSS	Pancreas	Pancrea
22	chr3:53924800-53926600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr3:53924800-53926600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:53924800-53926600	Active TSS	Esophagus	oesophagus
25	chr3:53924800-53926600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr3:53924800-53926800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:53924800-53926800	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr3:53924800-53926800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:53924800-53926800	Active TSS	Fetal Muscle Trunk	muscle
30	chr3:53924800-53927000	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr3:53925000-53926400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:53925000-53926400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:53925000-53926400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:53925000-53926400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:53925000-53926400	Active TSS	Fetal Intestine Small	intestine
36	chr3:53925000-53926400	Active TSS	Ovary	ovary
37	chr3:53925000-53926400	Active TSS	Small Intestine	intestine
38	chr3:53925000-53926400	Active TSS	NHDF-Ad	bronchial
39	chr3:53925000-53926600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:53925000-53926600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:53925000-53926600	Active TSS	Placenta Amnion	Placenta Amnion
42	chr3:53925000-53926600	Active TSS	HSMM	muscle
43	chr3:53925000-53926600	Active TSS	K562	blood
44	chr3:53925000-53926800	Active TSS	H9 Cell Line	embryonic stem cell
45	chr3:53925000-53926800	Active TSS	Brain Hippocampus Middle	brain
46	chr3:53925000-53926800	Active TSS	Left Ventricle	heart
47	chr3:53925000-53926800	Active TSS	NHLF	lung
48	chr3:53925000-53927000	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr3:53925200-53926400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:53925200-53926400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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