Variant report

Variant	rs41297941
Chromosome Location	chr4:129209851-129209852
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	chr4:129208341-129210330	K562	blood:	n/a	n/a
2	POLR2A	chr4:129207711-129210246	GM18951	blood:	n/a	n/a
3	MAX	chr4:129208824-129210017	HepG2	liver:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
4	POLR2A	chr4:129208264-129210305	HepG2	liver:	n/a	n/a
5	MAX	chr4:129208769-129210156	Hela-S3	cervix:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
6	POLR2A	chr4:129208554-129209923	U87	brain:	n/a	n/a
7	NFIC	chr4:129209249-129210231	GM12878	blood:	n/a	n/a
8	MYC	chr4:129208924-129210414	MCF10A-Er-Src	breast:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
9	POLR2A	chr4:129208257-129209907	K562	blood:	n/a	n/a
10	REST	chr4:129208417-129210480	H1-neurons	neurons:	n/a	n/a
11	MAX	chr4:129208644-129209958	HCT-116	colon:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
12	TAF1	chr4:129208503-129209892	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr4:129208318-129210364	Raji	blood:	n/a	n/a
14	MYC	chr4:129208768-129210294	K562	blood:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
15	POLR2A	chr4:129208554-129210025	GM12878	blood:	n/a	n/a
16	EBF1	chr4:129209139-129210063	GM12878	blood:	n/a	n/a
17	RUNX3	chr4:129209003-129209978	GM12878	blood:	n/a	n/a
18	NR2F2	chr4:129208978-129210099	K562	blood:	n/a	n/a
19	MTA3	chr4:129209125-129210466	GM12878	blood:	n/a	n/a
20	UBTF	chr4:129207914-129210111	K562	blood:	n/a	n/a
21	MAX	chr4:129208887-129209852	K562	blood:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
22	TRIM28	chr4:129208978-129210262	K562	blood:	n/a	chr4:129209720-129209728 chr4:129209696-129209704
23	POLR2A	chr4:129207453-129210280	HepG2	liver:	n/a	n/a
24	GATA3	chr4:129208978-129209942	MCF-7	breast:	n/a	n/a
25	POLR2A	chr4:129209798-129210228	GM12892	blood:	n/a	n/a
26	CREB1	chr4:129208699-129210075	H1-hESC	embryonic stem cell:	n/a	n/a
27	EP300	chr4:129208520-129210346	ECC-1	luminal epithelium:	n/a	chr4:129209768-129209781
28	HA-E2F1	chr4:129209049-129210094	MCF-7	breast:	n/a	chr4:129209106-129209118 chr4:129209373-129209382 chr4:129209050-129209059 chr4:129209482-129209492
29	POLR2A	chr4:129208541-129210320	K562	blood:	n/a	n/a
30	PML	chr4:129208735-129210277	GM12878	blood:	n/a	chr4:129209720-129209728 chr4:129209696-129209704
31	POLR2A	chr4:129208743-129211434	K562	blood:	n/a	n/a
32	NFIC	chr4:129209088-129210061	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr4:129208705-129210224	HL-60	blood:	n/a	n/a
34	NFATC1	chr4:129209207-129209968	GM12878	blood:	n/a	n/a
35	E2F6	chr4:129208913-129210229	A549	lung:	n/a	chr4:129208974-129208983 chr4:129209106-129209118 chr4:129209373-129209382 chr4:129209003-129209013 chr4:129209050-129209059 chr4:129209482-129209492 chr4:129209424-129209435 chr4:129208971-129208983
36	E2F6	chr4:129208368-129210391	K562	blood:	n/a	chr4:129208974-129208983 chr4:129209106-129209118 chr4:129209373-129209382 chr4:129209003-129209013 chr4:129209050-129209059 chr4:129209482-129209492 chr4:129209424-129209435 chr4:129208971-129208983
37	YY1	chr4:129208216-129209854	HepG2	liver:	n/a	chr4:129209050-129209059 chr4:129208394-129208405 chr4:129209478-129209492 chr4:129209478-129209487 chr4:129209476-129209487 chr4:129209475-129209489 chr4:129208974-129208983
38	SMC3	chr4:129208861-129210027	Hela-S3	cervix:	n/a	chr4:129208976-129208986
39	POLR2A	chr4:129208149-129210282	ProgFib	skin:	n/a	n/a
40	POLR2A	chr4:129208305-129210133	NB4	blood:	n/a	n/a
41	MAX	chr4:129208703-129210347	H1-hESC	embryonic stem cell:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
42	EP300	chr4:129209314-129210200	GM12878	blood:	n/a	chr4:129209768-129209781
43	MAX	chr4:129208723-129210273	SK-N-SH	brain:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
44	POLR2A	chr4:129208209-129210338	K562	blood:	n/a	n/a
45	STAT3	chr4:129209550-129210086	MCF10A-Er-Src	breast:	n/a	chr4:129209683-129209692 chr4:129209684-129209693
46	ZNF143	chr4:129208933-129209903	Hela-S3	cervix:	n/a	chr4:129208965-129208983 chr4:129209482-129209492
47	MAX	chr4:129208589-129210088	K562	blood:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
48	MAZ	chr4:129207095-129210225	IMR90	lung:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
49	RFX5	chr4:129208886-129209962	Hela-S3	cervix:	n/a	chr4:129209570-129209578
50	MAX	chr4:129208242-129210429	HepG2	liver:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120

No.	Distal block	Cell Line	Cell type
1	chr4:129209335..129213237-chr4:129730288..129733311,3	K562	blood:
2	chr4:128981698..128985397-chr4:129207989..129210555,4	K562	blood:
3	chr4:128980817..128984026-chr4:129207052..129210590,3	MCF-7	breast:
4	chr4:129208995..129209861-chr6:26123953..26124669,2	Hela-S3	cervix:
5	chr4:129191253..129196346-chr4:129207111..129210585,6	MCF-7	breast:
6	chr4:129208294..129210116-chr4:129731375..129734707,3	MCF-7	breast:

Variant related genes	Relation type
PGRMC2	TF binding region
ENSG00000251432	TF binding region
ENSG00000180573	Chromatin interaction
ENSG00000138709	Chromatin interaction
ENSG00000077684	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000164040	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28522979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28726176	1.00[AFR][1000 genomes]
rs59457552	1.00[AMR][1000 genomes]
rs60168588	1.00[AMR][1000 genomes]
rs6856379	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	esv3421519	chr4:129208027-129210875	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129204800-129210800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:129205200-129210000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:129205600-129210400	Active TSS	Fetal Intestine Small	intestine
4	chr4:129205600-129210600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr4:129205800-129210000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:129205800-129210200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr4:129205800-129210200	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr4:129205800-129210600	Active TSS	Fetal Brain Female	brain
9	chr4:129206000-129210000	Active TSS	Fetal Stomach	stomach
10	chr4:129206000-129210000	Active TSS	NHLF	lung
11	chr4:129206000-129210200	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr4:129206000-129210200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:129206000-129210400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:129206000-129210400	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr4:129206000-129210400	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr4:129206000-129210400	Active TSS	Fetal Intestine Large	intestine
17	chr4:129206000-129210400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr4:129206000-129210600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr4:129206000-129210600	Active TSS	A549	lung
20	chr4:129206200-129210200	Active TSS	Colonic Mucosa	Colon
21	chr4:129206200-129210400	Active TSS	Right Ventricle	heart
22	chr4:129206400-129210000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:129206400-129210000	Active TSS	NHDF-Ad	bronchial
24	chr4:129206400-129210200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:129206400-129210400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:129206600-129210000	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr4:129206600-129210200	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr4:129206800-129210000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:129206800-129210000	Active TSS	Brain Germinal Matrix	brain
30	chr4:129206800-129210200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr4:129206800-129210200	Active TSS	Ovary	ovary
32	chr4:129206800-129210400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:129206800-129211000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:129207000-129210000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:129207000-129210400	Active TSS	Placenta Amnion	Placenta Amnion
36	chr4:129207000-129210800	Active TSS	GM12878-XiMat	blood
37	chr4:129207200-129210000	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr4:129207200-129210000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:129207200-129210000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:129207200-129210400	Active TSS	Aorta	Aorta
41	chr4:129207200-129210400	Active TSS	Thymus	Thymus
42	chr4:129207400-129210000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:129207400-129210000	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr4:129207400-129210200	Active TSS	Stomach Smooth Muscle	stomach
45	chr4:129207400-129210400	Active TSS	H9 Cell Line	embryonic stem cell
46	chr4:129207400-129210400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:129207400-129210400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:129207400-129210400	Active TSS	Psoas Muscle	Psoas
49	chr4:129207600-129210000	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr4:129207600-129210000	Active TSS	Fetal Kidney	kidney

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