Variant report

Variant	rs57592932
Chromosome Location	chr3:53926461-53926462
allele	C/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	chr3:53925563-53926613	U87	brain:	n/a	n/a
2	MAX	chr3:53925506-53926572	A549	lung:	n/a	n/a
3	SRF	chr3:53925475-53926530	HCT-116	colon:	n/a	n/a
4	CHD1	chr3:53926236-53926528	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:53925214-53926549	Hela-S3	cervix:	n/a	n/a
6	E2F6	chr3:53925457-53926636	K562	blood:	n/a	n/a
7	PML	chr3:53925445-53926480	GM12878	blood:	n/a	n/a
8	CREB1	chr3:53924970-53926510	K562	blood:	n/a	n/a
9	POLR2A	chr3:53925489-53926467	Gliobla	brain:	n/a	n/a
10	POLR2A	chr3:53923739-53926749	PBDE	blood:	n/a	n/a
11	MAX	chr3:53925706-53926750	H1-hESC	embryonic stem cell:	n/a	n/a
12	USF2	chr3:53925721-53926631	GM12878	blood:	n/a	n/a
13	PBX3	chr3:53925604-53926533	SK-N-SH	brain:	n/a	chr3:53925952-53925961
14	GTF2F1	chr3:53925737-53926650	Hela-S3	cervix:	n/a	n/a
15	EP300	chr3:53925714-53926481	GM12878	blood:	n/a	n/a
16	HCFC1	chr3:53924769-53926647	Hela-S3	cervix:	n/a	n/a
17	CREB1	chr3:53924904-53926530	HepG2	liver:	n/a	n/a
18	POLR2A	chr3:53923021-53926962	IMR90	lung:	n/a	n/a
19	SIN3AK20	chr3:53925536-53926520	MCF-7	breast:	n/a	n/a
20	MAX	chr3:53925645-53926552	HepG2	liver:	n/a	n/a
21	ZKSCAN1	chr3:53925198-53926593	Hela-S3	cervix:	n/a	n/a
22	MAFK	chr3:53924941-53926492	Hela-S3	cervix:	n/a	chr3:53925920-53925935 chr3:53925920-53925931 chr3:53925296-53925311 chr3:53925920-53925931 chr3:53925921-53925932 chr3:53925920-53925936 chr3:53925921-53925932 chr3:53925919-53925933
23	NFYB	chr3:53925715-53926485	Hela-S3	cervix:	n/a	chr3:53925950-53925964 chr3:53925949-53925964 chr3:53925951-53925966 chr3:53925952-53925962 chr3:53925949-53925964
24	GABPA	chr3:53925441-53926610	MCF-7	breast:	n/a	n/a
25	JUND	chr3:53925717-53926485	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr3:53925723-53926663	A549	lung:	n/a	n/a
27	POLR2A	chr3:53925669-53926611	K562	blood:	n/a	n/a
28	CREB1	chr3:53924983-53926479	GM12878	blood:	n/a	n/a
29	RFX5	chr3:53924629-53926908	SK-N-SH	brain:	n/a	chr3:53925952-53925961
30	ELK1	chr3:53925710-53926554	Hela-S3	cervix:	n/a	n/a
31	BACH1	chr3:53925862-53926461	K562	blood:	n/a	n/a
32	MAX	chr3:53925502-53926464	H1-hESC	embryonic stem cell:	n/a	n/a
33	MXI1	chr3:53926007-53926648	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr3:53925512-53926499	U87	brain:	n/a	n/a
35	REST	chr3:53924877-53926497	H1-neurons	neurons:	n/a	chr3:53925449-53925456
36	CREB1	chr3:53925386-53926484	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr3:53924112-53926945	MCF10A-Er-Src	breast:	n/a	n/a
38	REST	chr3:53924707-53927104	H1-neurons	neurons:	n/a	chr3:53925449-53925456
39	MAX	chr3:53925632-53926468	SK-N-SH	brain:	n/a	n/a
40	MAFK	chr3:53925731-53926559	K562	blood:	n/a	chr3:53925920-53925935 chr3:53925920-53925931 chr3:53925920-53925931 chr3:53925921-53925932 chr3:53925920-53925936 chr3:53925921-53925932 chr3:53925919-53925933
41	MXI1	chr3:53924781-53926914	IMR90	lung:	n/a	n/a
42	HCFC1	chr3:53925370-53926573	K562	blood:	n/a	n/a
43	ATF1	chr3:53925053-53926665	K562	blood:	n/a	n/a
44	TAF1	chr3:53925432-53926695	H1-neurons	neurons:	n/a	n/a
45	GABPA	chr3:53925673-53926468	A549	lung:	n/a	n/a
46	SMARCC1	chr3:53924959-53926671	Hela-S3	cervix:	n/a	n/a
47	ZMIZ1	chr3:53925625-53926726	K562	blood:	n/a	n/a
48	CHD1	chr3:53923633-53926732	IMR90	lung:	n/a	n/a
49	EGR1	chr3:53925514-53926489	HCT-116	colon:	n/a	chr3:53926128-53926135 chr3:53926022-53926033 chr3:53926022-53926036
50	MXI1	chr3:53925112-53926603	Hela-S3	cervix:	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	chr20:30193754..30194579-chr3:53926417..53926984,2	Hela-S3	cervix:
4	chr3:53909521..53911477-chr3:53924349..53927028,2	MCF-7	breast:
5	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
6	chr3:53913820..53918433-chr3:53924406..53927799,6	MCF-7	breast:

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

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12637033	0.90[AFR][1000 genomes]
rs2232339	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2232344	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28385746	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28385747	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28385748	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28385750	1.00[AFR][1000 genomes]
rs28385752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28741395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28741396	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28741399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28741401	0.90[AFR][1000 genomes]
rs28741402	0.90[AFR][1000 genomes]
rs56729512	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57504026	0.95[AFR][1000 genomes]
rs59514001	0.95[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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53923600-53926600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr3:53924200-53926600	Active TSS	Psoas Muscle	Psoas
3	chr3:53924200-53926600	Active TSS	Right Atrium	heart
4	chr3:53924200-53926800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:53924400-53926800	Active TSS	HSMMtube	muscle
6	chr3:53924600-53926600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr3:53924600-53926800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:53924600-53926800	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr3:53924600-53926800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:53924800-53926600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr3:53924800-53926600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:53924800-53926600	Active TSS	Esophagus	oesophagus
13	chr3:53924800-53926600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:53924800-53926800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:53924800-53926800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr3:53924800-53926800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:53924800-53926800	Active TSS	Fetal Muscle Trunk	muscle
18	chr3:53924800-53927000	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr3:53925000-53926600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:53925000-53926600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:53925000-53926600	Active TSS	Placenta Amnion	Placenta Amnion
22	chr3:53925000-53926600	Active TSS	HSMM	muscle
23	chr3:53925000-53926600	Active TSS	K562	blood
24	chr3:53925000-53926800	Active TSS	H9 Cell Line	embryonic stem cell
25	chr3:53925000-53926800	Active TSS	Brain Hippocampus Middle	brain
26	chr3:53925000-53926800	Active TSS	Left Ventricle	heart
27	chr3:53925000-53926800	Active TSS	NHLF	lung
28	chr3:53925000-53927000	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr3:53925200-53926600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:53925200-53926600	Active TSS	Colon Smooth Muscle	Colon
31	chr3:53925200-53926600	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr3:53925200-53926800	Active TSS	Brain Anterior Caudate	brain
33	chr3:53925200-53926800	Active TSS	Duodenum Mucosa	Duodenum
34	chr3:53925200-53926800	Active TSS	Fetal Lung	lung
35	chr3:53925200-53926800	Active TSS	A549	lung
36	chr3:53925200-53927000	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr3:53925400-53926600	Active TSS	Fetal Brain Female	brain
38	chr3:53925800-53926800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:53925800-53926800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:53925800-53926800	Active TSS	Brain Germinal Matrix	brain
41	chr3:53926000-53926600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:53926200-53926600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr3:53926200-53926600	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr3:53926200-53926600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr3:53926200-53926600	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr3:53926200-53926600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:53926200-53926600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr3:53926200-53926600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:53926200-53926600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr3:53926200-53926600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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