Variant report

Variant	rs534370936
Chromosome Location	chr4:3293426-3293427
allele	C/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	SIN3AK20	chr4:3293160-3294773	MCF-7	breast:	n/a	n/a
2	GABPA	chr4:3293267-3293868	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr4:3293337-3297140	HepG2	liver:	n/a	n/a
4	HA-E2F1	chr4:3293257-3294560	MCF-7	breast:	n/a	chr4:3294103-3294112 chr4:3293858-3293870 chr4:3293969-3293979 chr4:3294491-3294500
5	REST	chr4:3293209-3295708	H1-neurons	neurons:	n/a	chr4:3293975-3293988 chr4:3294439-3294453 chr4:3294441-3294451 chr4:3293979-3293988 chr4:3294057-3294070 chr4:3293992-3294005 chr4:3293972-3293985 chr4:3294443-3294456 chr4:3295683-3295701
6	CTCF	chr4:3293420-3293570	SAEC	small airway:	n/a	n/a
7	CREB1	chr4:3293236-3294971	HepG2	liver:	n/a	n/a
8	MXI1	chr4:3293305-3295574	IMR90	lung:	n/a	n/a
9	SIN3A	chr4:3293331-3294968	H1-hESC	embryonic stem cell:	n/a	chr4:3294441-3294450 chr4:3294054-3294067
10	TCF12	chr4:3293245-3294631	ECC-1	luminal epithelium:	n/a	chr4:3294554-3294564
11	CTCF	chr4:3293400-3293550	HMEC	breast:	n/a	n/a
12	TCF12	chr4:3293228-3294621	ECC-1	luminal epithelium:	n/a	chr4:3294554-3294564
13	POLR2A	chr4:3293422-3293492	MCF-7	breast:	n/a	n/a
14	POLR2A	chr4:3293394-3295339	Hela-S3	cervix:	n/a	n/a
15	STAT3	chr4:3293414-3293699	MCF10A-Er-Src	breast:	n/a	n/a
16	CTCF	chr4:3293420-3293570	HMEC	breast:	n/a	n/a
17	MYC	chr4:3293417-3293678	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr4:3293423-3295472	MCF10A-Er-Src	breast:	n/a	n/a
19	MAX	chr4:3293168-3294827	HepG2	liver:	n/a	n/a
20	MAX	chr4:3293327-3294771	MCF-7	breast:	n/a	n/a
21	MAZ	chr4:3293336-3295820	IMR90	lung:	n/a	n/a
22	E2F4	chr4:3293346-3294675	MCF10A-Er-Src	breast:	n/a	chr4:3294103-3294112 chr4:3293858-3293870 chr4:3293969-3293979 chr4:3294491-3294500
23	POLR2A	chr4:3292258-3296142	HepG2	liver:	n/a	n/a
24	MYBL2	chr4:3293388-3294687	HepG2	liver:	n/a	n/a
25	GATA3	chr4:3293316-3293596	T-47D	breast:	n/a	n/a
26	NFIC	chr4:3293195-3294629	ECC-1	luminal epithelium:	n/a	chr4:3293688-3293704
27	SMC3	chr4:3293379-3293581	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr4:3293417-3293486	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr4:3293421-3293562	Hela-S3	cervix:	n/a	n/a
30	MXI1	chr4:3293409-3295194	HepG2	liver:	n/a	n/a
31	NFIC	chr4:3293230-3294622	ECC-1	luminal epithelium:	n/a	chr4:3293688-3293704
32	STAT3	chr4:3293412-3293748	MCF10A-Er-Src	breast:	n/a	n/a
33	MXI1	chr4:3293056-3296207	SK-N-SH	brain:	n/a	n/a
34	MYC	chr4:3293424-3293543	MCF-7	breast:	n/a	n/a
35	POLR2A	chr4:3293312-3295798	H1-neurons	neurons:	n/a	n/a
36	MAX	chr4:3293251-3294808	ECC-1	luminal epithelium:	n/a	n/a
37	MAX	chr4:3293243-3296204	HepG2	liver:	n/a	n/a
38	BHLHE40	chr4:3293310-3294186	HepG2	liver:	n/a	chr4:3294055-3294071 chr4:3293992-3294008
39	CTCF	chr4:3293380-3293530	HepG2	liver:	n/a	n/a
40	MAX	chr4:3293257-3294767	ECC-1	luminal epithelium:	n/a	n/a
41	SMARCB1	chr4:3293379-3294526	Hela-S3	cervix:	n/a	n/a
42	STAT3	chr4:3293413-3293955	MCF10A-Er-Src	breast:	n/a	chr4:3293881-3293889

No.	Distal block	Cell Line	Cell type
1	chr4:3292471..3295854-chr4:3462941..3467927,8	MCF-7	breast:
2	chr4:3292102..3294475-chr4:3451973..3453863,2	MCF-7	breast:
3	chr4:3284056..3285844-chr4:3292232..3294141,2	MCF-7	breast:
4	chr4:3233193..3236137-chr4:3292325..3293850,2	MCF-7	breast:
5	chr4:3292635..3294292-chr4:3500969..3502505,2	MCF-7	breast:
6	chr4:3283519..3286259-chr4:3292639..3294370,2	K562	blood:
7	chr4:3292637..3295776-chr4:3483843..3488274,4	MCF-7	breast:
8	chr4:3074885..3077461-chr4:3292207..3294882,2	MCF-7	breast:
9	chr4:3269278..3270856-chr4:3292386..3294072,2	MCF-7	breast:
10	chr4:3292758..3295748-chr4:3341243..3344299,3	MCF-7	breast:

Variant related genes	Relation type
RGS12	TF binding region
ENSG00000159788	Chromatin interaction
ENSG00000175920	Chromatin interaction
ENSG00000197386	Chromatin interaction
ENSG00000251075	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv878454	chr4:3215835-3305739	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv878458	chr4:3235518-3303976	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv878459	chr4:3235518-3310831	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv878460	chr4:3260154-3303976	Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv878461	chr4:3270488-3339038	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv593440	chr4:3283422-3339038	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv461165	chr4:3283422-3342137	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
14	nsv593441	chr4:3283422-3342137	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
15	esv3400837	chr4:3293379-3295927	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3292600-3294000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr4:3292600-3294400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr4:3292600-3295600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:3292800-3293800	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr4:3292800-3294000	Enhancers	Fetal Brain Male	brain
6	chr4:3293000-3293600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:3293000-3293600	Flanking Active TSS	HepG2	liver
8	chr4:3293000-3293800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:3293000-3293800	Weak transcription	Small Intestine	intestine
10	chr4:3293000-3294000	Flanking Active TSS	Right Ventricle	heart
11	chr4:3293000-3294200	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr4:3293000-3295600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:3293200-3293600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:3293200-3293600	Bivalent Enhancer	Primary B cells from cord blood	blood
15	chr4:3293200-3293600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
16	chr4:3293200-3293600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:3293200-3293600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr4:3293200-3293600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:3293200-3293600	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr4:3293200-3293600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:3293200-3293600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr4:3293200-3293600	Flanking Active TSS	Fetal Brain Female	brain
23	chr4:3293200-3293600	Flanking Active TSS	Fetal Kidney	kidney
24	chr4:3293200-3293600	Bivalent Enhancer	Fetal Thymus	thymus
25	chr4:3293200-3293600	Flanking Active TSS	Left Ventricle	heart
26	chr4:3293200-3293600	Flanking Active TSS	Ovary	ovary
27	chr4:3293200-3293600	Flanking Active TSS	Pancreas	Pancrea
28	chr4:3293200-3293600	Bivalent/Poised TSS	Thymus	Thymus
29	chr4:3293200-3293800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:3293200-3293800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:3293200-3293800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
32	chr4:3293200-3293800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr4:3293200-3293800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr4:3293200-3293800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:3293200-3293800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:3293200-3293800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:3293200-3293800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:3293200-3293800	Flanking Active TSS	Brain Angular Gyrus	brain
39	chr4:3293200-3293800	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr4:3293200-3293800	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr4:3293200-3293800	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr4:3293200-3293800	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr4:3293200-3293800	Flanking Active TSS	Fetal Intestine Large	intestine
44	chr4:3293200-3293800	Flanking Active TSS	Fetal Intestine Small	intestine
45	chr4:3293200-3293800	Flanking Active TSS	Fetal Lung	lung
46	chr4:3293200-3293800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr4:3293200-3293800	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr4:3293200-3294000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr4:3293200-3294000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr4:3293200-3294000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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