Variant report

Variant	rs3025802
Chromosome Location	chr4:3247544-3247545
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	chr4:3245779-3248772	GM19193	blood:	n/a	n/a
2	POLR2A	chr4:3247506-3247766	GM12892	blood:	n/a	n/a
3	POLR2A	chr4:3245637-3248092	GM12892	blood:	n/a	n/a
4	POLR2A	chr4:3246442-3247751	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:3244619-3248406	GM12891	blood:	n/a	n/a
6	POLR2A	chr4:3244931-3248642	GM18505	blood:	n/a	n/a
7	POLR2A	chr4:3244102-3248493	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:3245513-3247771	GM15510	blood:	n/a	n/a
9	MTA3	chr4:3245374-3247599	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:3246780-3247635	MCF-7	breast:	n/a	n/a
11	POLR2A	chr4:3245597-3247902	GM12891	blood:	n/a	n/a
12	POLR2A	chr4:3245740-3247727	GM18951	blood:	n/a	n/a
13	POLR2A	chr4:3244712-3247939	GM12892	blood:	n/a	n/a
14	POLR2A	chr4:3245953-3247652	Hela-S3	cervix:	n/a	n/a
15	STAT5A	chr4:3247306-3247814	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:3244651-3247810	GM12891	blood:	n/a	n/a
17	POLR2A	chr4:3246753-3247821	GM12878	blood:	n/a	n/a
18	POLR2A	chr4:3245653-3248647	GM12891	blood:	n/a	n/a
19	POLR2A	chr4:3246611-3247847	GM12878	blood:	n/a	n/a
20	POLR2A	chr4:3245039-3247602	K562	blood:	n/a	n/a
21	POLR2A	chr4:3247450-3247653	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr4:3244754-3248080	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3243758..3245995-chr4:3246893..3248968,3	K562	blood:
2	chr4:3075638..3077191-chr4:3246487..3249347,2	MCF-7	breast:

Variant related genes	Relation type
MSANTD1	TF binding region
ENSG00000197386	Chromatin interaction
ENSG00000251075	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs362291	1.00[AMR][1000 genomes]
rs363116	1.00[AMR][1000 genomes]
rs55937165	1.00[AMR][1000 genomes]
rs56082242	1.00[AMR][1000 genomes]
rs61547416	1.00[AMR][1000 genomes]
rs73792357	1.00[AMR][1000 genomes]
rs73792373	1.00[AMR][1000 genomes]
rs73792377	1.00[AMR][1000 genomes]
rs73792379	1.00[AMR][1000 genomes]
rs73792381	1.00[AMR][1000 genomes]
rs73792382	1.00[AMR][1000 genomes]
rs73792386	1.00[AMR][1000 genomes]
rs73792387	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv524211	chr4:3215835-3270488	Strong transcription Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv470003	chr4:3215835-3275484	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	nsv878457	chr4:3231661-3278517	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
11	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
12	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

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3213800-3247600	Strong transcription	Primary T cells from cord blood	blood
3	chr4:3223400-3247600	Strong transcription	Fetal Brain Female	brain
4	chr4:3238000-3259200	Weak transcription	HSMMtube	muscle
5	chr4:3238200-3250200	Weak transcription	Fetal Brain Male	brain
6	chr4:3238200-3255200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:3238200-3261400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:3238600-3259800	Weak transcription	NH-A	brain
9	chr4:3239800-3247600	Genic enhancers	Fetal Stomach	stomach
10	chr4:3241600-3259200	Weak transcription	Small Intestine	intestine
11	chr4:3242200-3248800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:3242200-3252000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:3243000-3247800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:3243000-3260000	Weak transcription	Brain Angular Gyrus	brain
15	chr4:3243200-3251400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:3243400-3247600	Weak transcription	Osteobl	bone
17	chr4:3243400-3248600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr4:3243400-3250400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:3243400-3252000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:3243400-3254400	Weak transcription	GM12878-XiMat	blood
21	chr4:3243400-3259200	Weak transcription	Colonic Mucosa	Colon
22	chr4:3243400-3259600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:3243600-3247800	Weak transcription	Brain Substantia Nigra	brain
24	chr4:3243600-3258800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr4:3243800-3257400	Weak transcription	Gastric	stomach
26	chr4:3243800-3258000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:3244000-3248400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:3244000-3252200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr4:3244000-3252200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:3244200-3248200	Weak transcription	HepG2	liver
31	chr4:3244200-3252400	Weak transcription	Fetal Intestine Large	intestine
32	chr4:3244200-3259400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:3244400-3252000	Weak transcription	Fetal Lung	lung
34	chr4:3244600-3248200	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:3244800-3250000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:3244800-3251200	Weak transcription	Brain Anterior Caudate	brain
37	chr4:3244800-3259600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:3245000-3247600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:3245000-3255400	Weak transcription	Esophagus	oesophagus
40	chr4:3245200-3247600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr4:3245200-3247800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr4:3245200-3248000	Weak transcription	Placenta	Placenta
43	chr4:3245200-3248200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:3245200-3251800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr4:3245200-3255000	Weak transcription	Pancreas	Pancrea
46	chr4:3245200-3259800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr4:3245200-3260000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr4:3245400-3248200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr4:3245400-3256600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:3245400-3257800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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