Variant report

Variant	rs4467424
Chromosome Location	chr3:42553262-42553263
allele	G/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	EBF1	chr3:42553201-42553482	GM12878	blood:	n/a	chr3:42553357-42553370 chr3:42553358-42553369
2	EBF1	chr3:42553169-42553574	GM12878	blood:	n/a	chr3:42553357-42553370 chr3:42553358-42553369

No.	Distal block	Cell Line	Cell type
1	chr3:42542685..42546162-chr3:42551658..42554598,5	MCF-7	breast:
2	chr3:42542637..42545106-chr3:42553030..42555271,2	K562	blood:
3	chr3:42552045..42554738-chr3:42559579..42561082,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEC22C-1	chr3:42553207-42553401	ENSG00000232354.3
2	lnc-SEC22C-1	chr3:42553207-42553401	ENSG00000232354.3

Variant related genes	Relation type
VIPR1	TF binding region
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13321590	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030440	1.00[MEX][hapmap]
rs7613206	1.00[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7628932	0.88[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs95923	0.86[AFR][1000 genomes];1.00[AMR][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	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv527430	chr3:42534042-42557199	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42545400-42553800	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr3:42546600-42553800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr3:42547200-42561800	Genic enhancers	Fetal Intestine Small	intestine
4	chr3:42547600-42579000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:42549200-42561800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:42549400-42555800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:42549800-42557000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:42549800-42560600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:42550000-42556000	Weak transcription	Brain Anterior Caudate	brain
10	chr3:42550000-42560400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:42550200-42553600	Genic enhancers	Primary T cells from cord blood	blood
12	chr3:42550200-42558200	Enhancers	Right Ventricle	heart
13	chr3:42550400-42555000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:42550400-42555600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:42550600-42555000	Enhancers	Adipose Nuclei	Adipose
16	chr3:42550600-42558800	Enhancers	Right Atrium	heart
17	chr3:42550800-42555600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:42551000-42553600	Enhancers	Fetal Intestine Large	intestine
19	chr3:42551200-42559200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:42551400-42554000	Enhancers	Placenta	Placenta
21	chr3:42551400-42554000	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr3:42551400-42554200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr3:42551400-42558800	Enhancers	Left Ventricle	heart
24	chr3:42551600-42553800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:42551600-42555400	Enhancers	Aorta	Aorta
26	chr3:42551800-42553800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr3:42551800-42554000	Enhancers	Primary T cells fromperipheralblood	blood
28	chr3:42551800-42554400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr3:42552000-42553600	Enhancers	Lung	lung
30	chr3:42552200-42555600	Weak transcription	Fetal Heart	heart
31	chr3:42552200-42556400	Weak transcription	Gastric	stomach
32	chr3:42552200-42581000	Weak transcription	Pancreas	Pancrea
33	chr3:42552400-42553600	Weak transcription	Colonic Mucosa	Colon
34	chr3:42552400-42554800	Enhancers	Duodenum Mucosa	Duodenum
35	chr3:42552400-42558400	Genic enhancers	Rectal Mucosa Donor 31	rectum
36	chr3:42552400-42570000	Weak transcription	Fetal Stomach	stomach
37	chr3:42552600-42553400	Weak transcription	Liver	Liver
38	chr3:42552600-42553600	Enhancers	Primary B cells from cord blood	blood
39	chr3:42552600-42554000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr3:42552800-42553600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:42553000-42553400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:42553000-42553800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr3:42553000-42554000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr3:42553000-42554600	Weak transcription	Stomach Mucosa	stomach
45	chr3:42553000-42555800	Weak transcription	Esophagus	oesophagus
46	chr3:42553000-42556200	Weak transcription	Brain Hippocampus Middle	brain
47	chr3:42553200-42553400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
48	chr3:42553200-42553400	Enhancers	Spleen	Spleen
49	chr3:42553200-42553600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:42553200-42553800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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