Variant report

Variant	rs369538489
Chromosome Location	chr4:129208665-129208666
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	POLR2A	chr4:129208341-129210330	K562	blood:	n/a	n/a
2	POLR2A	chr4:129207711-129210246	GM18951	blood:	n/a	n/a
3	YY1	chr4:129208664-129209068	GM12892	blood:	n/a	chr4:129209050-129209059 chr4:129208974-129208983
4	POLR2A	chr4:129208264-129210305	HepG2	liver:	n/a	n/a
5	POLR2A	chr4:129208554-129209923	U87	brain:	n/a	n/a
6	POLR2A	chr4:129208257-129209907	K562	blood:	n/a	n/a
7	REST	chr4:129208417-129210480	H1-neurons	neurons:	n/a	n/a
8	MAX	chr4:129208644-129209958	HCT-116	colon:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
9	TAF1	chr4:129208503-129209892	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr4:129208318-129210364	Raji	blood:	n/a	n/a
11	POLR2A	chr4:129208554-129210025	GM12878	blood:	n/a	n/a
12	UBTF	chr4:129207914-129210111	K562	blood:	n/a	n/a
13	YY1	chr4:129208469-129209671	GM12878	blood:	n/a	chr4:129209050-129209059 chr4:129209478-129209492 chr4:129209478-129209487 chr4:129209476-129209487 chr4:129209475-129209489 chr4:129208974-129208983
14	SIN3AK20	chr4:129208664-129209127	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr4:129207453-129210280	HepG2	liver:	n/a	n/a
16	EP300	chr4:129208520-129210346	ECC-1	luminal epithelium:	n/a	chr4:129209768-129209781
17	POLR2A	chr4:129208301-129208680	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr4:129208541-129210320	K562	blood:	n/a	n/a
19	TBP	chr4:129208537-129209704	Hela-S3	cervix:	n/a	n/a
20	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
21	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
22	POLR2A	chr4:129208149-129210282	ProgFib	skin:	n/a	n/a
23	POLR2A	chr4:129208305-129210133	NB4	blood:	n/a	n/a
24	POLR2A	chr4:129208209-129210338	K562	blood:	n/a	n/a
25	MAX	chr4:129208589-129210088	K562	blood:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
26	SMARCB1	chr4:129207867-129209820	Hela-S3	cervix:	n/a	n/a
27	MAZ	chr4:129207095-129210225	IMR90	lung:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
28	TAF1	chr4:129208303-129209813	A549	lung:	n/a	n/a
29	MAX	chr4:129208242-129210429	HepG2	liver:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
30	POLR2A	chr4:129208197-129209901	GM19193	blood:	n/a	n/a
31	POLR2A	chr4:129208345-129209825	H1-neurons	neurons:	n/a	n/a
32	POLR2A	chr4:129208632-129210288	GM15510	blood:	n/a	n/a
33	TAF1	chr4:129208383-129208672	H1-hESC	embryonic stem cell:	n/a	n/a
34	SIN3AK20	chr4:129208585-129209915	MCF-7	breast:	n/a	n/a
35	POLR2A	chr4:129208582-129209834	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr4:129208363-129209673	HepG2	liver:	n/a	n/a
37	EP300	chr4:129208555-129209843	SK-N-SH	brain:	n/a	chr4:129209768-129209781
38	MAX	chr4:129208292-129208687	H1-hESC	embryonic stem cell:	n/a	n/a
39	MYC	chr4:129208312-129210214	K562	blood:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
40	MXI1	chr4:129208437-129209830	Hela-S3	cervix:	n/a	chr4:129209521-129209530
41	RCOR1	chr4:129208420-129209702	K562	blood:	n/a	n/a
42	POLR2A	chr4:129208528-129210502	SK-N-MC	brain:	n/a	n/a
43	POLR2A	chr4:129208303-129209878	MCF-7	breast:	n/a	n/a
44	POLR2A	chr4:129208470-129209911	PFSK-1	brain:	n/a	n/a
45	MAX	chr4:129208292-129210342	H1-hESC	embryonic stem cell:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
46	HA-E2F1	chr4:129208616-129209757	Hela-S3	cervix:	n/a	chr4:129208974-129208983 chr4:129209106-129209118 chr4:129209373-129209382 chr4:129209003-129209013 chr4:129209050-129209059 chr4:129209482-129209492 chr4:129208971-129208983
47	MAZ	chr4:129208324-129210257	K562	blood:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
48	E2F4	chr4:129208270-129209705	K562	blood:	n/a	chr4:129208974-129208983 chr4:129209106-129209118 chr4:129209373-129209382 chr4:129209424-129209435 chr4:129209003-129209013 chr4:129209050-129209059 chr4:129209482-129209492 chr4:129208971-129208983
49	TAF1	chr4:129208229-129208676	HepG2	liver:	n/a	n/a
50	POLR2A	chr4:129208606-129210379	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:129208497..129209007-chr5:36241002..36241648,2	NB4	blood:
2	chr4:129207739..129209319-chr4:129473480..129475503,2	MCF-7	breast:
3	chr4:129206178..129209498-chr4:129731212..129733921,5	K562	blood:
4	chr4:128981725..128985397-chr4:129207989..129209697,3	K562	blood:
5	chr4:128981698..128985397-chr4:129207989..129210555,4	K562	blood:
6	chr4:128980817..128984026-chr4:129207052..129210590,3	MCF-7	breast:
7	chr1:144533931..144534460-chr4:129208632..129209239,2	Hela-S3	cervix:
8	chr4:129191253..129196346-chr4:129207111..129210585,6	MCF-7	breast:
9	chr12:112819695..112820500-chr4:129208574..129209097,2	NB4	blood:
10	chr4:129208294..129210116-chr4:129731375..129734707,3	MCF-7	breast:
11	chr4:129206178..129209105-chr4:129728853..129732712,4	K562	blood:
12	chr12:29533777..29534329-chr4:129208370..129209099,2	Hela-S3	cervix:
13	chr4:129207558..129209105-chr4:129728853..129730896,2	K562	blood:
14	chr12:132674042..132674756-chr4:129208582..129209342,2	Hela-S3	cervix:

Variant related genes	Relation type
PGRMC2	TF binding region
ENSG00000138709	Chromatin interaction
ENSG00000273077	Chromatin interaction
ENSG00000087502	Chromatin interaction
ENSG00000164040	Chromatin interaction
ENSG00000173064	Chromatin interaction
ENSG00000152620	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000077684	Chromatin interaction
ENSG00000256576	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

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:127 , 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	chr4:129205400-129209800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:129205600-129210400	Active TSS	Fetal Intestine Small	intestine
5	chr4:129205600-129210600	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr4:129205800-129209800	Active TSS	Duodenum Mucosa	Duodenum
7	chr4:129205800-129210000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:129205800-129210200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr4:129205800-129210200	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr4:129205800-129210600	Active TSS	Fetal Brain Female	brain
11	chr4:129206000-129209200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:129206000-129209800	Active TSS	HSMMtube	muscle
13	chr4:129206000-129210000	Active TSS	Fetal Stomach	stomach
14	chr4:129206000-129210000	Active TSS	NHLF	lung
15	chr4:129206000-129210200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr4:129206000-129210200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:129206000-129210400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:129206000-129210400	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr4:129206000-129210400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr4:129206000-129210400	Active TSS	Fetal Intestine Large	intestine
21	chr4:129206000-129210400	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr4:129206000-129210600	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr4:129206000-129210600	Active TSS	A549	lung
24	chr4:129206200-129209800	Active TSS	Rectal Smooth Muscle	rectum
25	chr4:129206200-129209800	Active TSS	Hela-S3	cervix
26	chr4:129206200-129209800	Active TSS	HSMM	muscle
27	chr4:129206200-129210200	Active TSS	Colonic Mucosa	Colon
28	chr4:129206200-129210400	Active TSS	Right Ventricle	heart
29	chr4:129206400-129209800	Active TSS	H1 Cell Line	embryonic stem cell
30	chr4:129206400-129210000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:129206400-129210000	Active TSS	NHDF-Ad	bronchial
32	chr4:129206400-129210200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:129206400-129210400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:129206600-129209600	Active TSS	Placenta	Placenta
35	chr4:129206600-129210000	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr4:129206600-129210200	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr4:129206800-129209600	Active TSS	HMEC	breast
38	chr4:129206800-129209800	Active TSS	Muscle Satellite Cultured Cells	--
39	chr4:129206800-129210000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:129206800-129210000	Active TSS	Brain Germinal Matrix	brain
41	chr4:129206800-129210200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr4:129206800-129210200	Active TSS	Ovary	ovary
43	chr4:129206800-129210400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:129206800-129211000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:129207000-129209800	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr4:129207000-129209800	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr4:129207000-129210000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:129207000-129210400	Active TSS	Placenta Amnion	Placenta Amnion
49	chr4:129207000-129210800	Active TSS	GM12878-XiMat	blood
50	chr4:129207200-129209600	Active TSS	Fetal Muscle Trunk	muscle

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