Variant report

Variant	rs28522979
Chromosome Location	chr4:129209315-129209316
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	POLR2A	chr4:129208341-129210330	K562	blood:	n/a	n/a
2	MAFK	chr4:129209195-129209395	HepG2	liver:	n/a	n/a
3	YY1	chr4:129208707-129209674	GM12892	blood:	n/a	chr4:129209050-129209059 chr4:129209478-129209492 chr4:129209478-129209487 chr4:129209476-129209487 chr4:129209475-129209489 chr4:129208974-129208983
4	USF1	chr4:129209029-129209662	H1-hESC	embryonic stem cell:	n/a	chr4:129209481-129209497 chr4:129209475-129209491
5	CREB1	chr4:129208709-129209791	H1-hESC	embryonic stem cell:	n/a	n/a
6	ATF3	chr4:129209184-129209667	K562	blood:	n/a	n/a
7	PAX5	chr4:129208719-129209679	GM12892	blood:	n/a	chr4:129209373-129209382
8	POLR2A	chr4:129209167-129209717	U87	brain:	n/a	n/a
9	E2F4	chr4:129209190-129209588	GM12878	blood:	n/a	chr4:129209373-129209382 chr4:129209424-129209435 chr4:129209482-129209492
10	MAX	chr4:129208966-129209753	HUVEC	blood vessel:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
11	CTCF	chr4:129209280-129209430	SAEC	small airway:	n/a	n/a
12	MYBL2	chr4:129209016-129209836	HepG2	liver:	n/a	n/a
13	NRF1	chr4:129209032-129209593	H1-hESC	embryonic stem cell:	n/a	chr4:129209372-129209383 chr4:129209136-129209147 chr4:129209136-129209145 chr4:129209372-129209383 chr4:129209372-129209386 chr4:129209050-129209059 chr4:129209153-129209162 chr4:129209369-129209383
14	POLR2A	chr4:129207711-129210246	GM18951	blood:	n/a	n/a
15	POLR2A	chr4:129209155-129209741	HepG2	liver:	n/a	n/a
16	SP1	chr4:129208827-129209664	H1-hESC	embryonic stem cell:	n/a	chr4:129209049-129209061 chr4:129209265-129209276 chr4:129209153-129209162 chr4:129209152-129209161 chr4:129209151-129209163 chr4:129208972-129208984 chr4:129209007-129209016 chr4:129209152-129209162 chr4:129208974-129208983 chr4:129208965-129208979 chr4:129209006-129209018 chr4:129209151-129209163 chr4:129209050-129209060 chr4:129209109-129209118 chr4:129208973-129208987 chr4:129209008-129209017 chr4:129209427-129209441 chr4:129209049-129209061 chr4:129209050-129209059 chr4:129208973-129208982 chr4:129209050-129209060 chr4:129208972-129208984 chr4:129209006-129209018 chr4:129209051-129209060 chr4:129208962-129208976 chr4:129209152-129209166 chr4:129209051-129209060 chr4:129209152-129209162 chr4:129209007-129209017 chr4:129209108-129209122 chr4:129208973-129208982
17	MAX	chr4:129208824-129210017	HepG2	liver:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
18	EGR1	chr4:129208926-129209757	ECC-1	luminal epithelium:	n/a	chr4:129209045-129209058 chr4:129209153-129209163 chr4:129209154-129209167 chr4:129209137-129209146 chr4:129209479-129209492 chr4:129208975-129208988 chr4:129209107-129209121 chr4:129209111-129209121 chr4:129209110-129209123 chr4:129209044-129209059 chr4:129209109-129209124 chr4:129209152-129209162 chr4:129209110-129209123 chr4:129209373-129209382 chr4:129209136-129209145 chr4:129209045-129209058
19	ZNF384	chr4:129209035-129209674	K562	blood:	n/a	n/a
20	POLR2A	chr4:129208264-129210305	HepG2	liver:	n/a	n/a
21	MAX	chr4:129208769-129210156	Hela-S3	cervix:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
22	HEY1	chr4:129209097-129209795	K562	blood:	n/a	n/a
23	NFIC	chr4:129209110-129209658	HepG2	liver:	n/a	n/a
24	ELF1	chr4:129208723-129209847	K562	blood:	n/a	chr4:129209001-129209013
25	POLR2A	chr4:129208712-129209754	SK-N-MC	brain:	n/a	n/a
26	CREB1	chr4:129208714-129209667	A549	lung:	n/a	n/a
27	POLR2A	chr4:129208554-129209923	U87	brain:	n/a	n/a
28	NFIC	chr4:129209249-129210231	GM12878	blood:	n/a	n/a
29	USF1	chr4:129209221-129209702	A549	lung:	n/a	chr4:129209481-129209497 chr4:129209475-129209491
30	MYC	chr4:129208924-129210414	MCF10A-Er-Src	breast:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
31	REST	chr4:129209265-129209614	SK-N-SH	brain:	n/a	n/a
32	BRCA1	chr4:129209122-129209580	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr4:129209083-129209688	A549	lung:	n/a	n/a
34	POLR2A	chr4:129208257-129209907	K562	blood:	n/a	n/a
35	REST	chr4:129208417-129210480	H1-neurons	neurons:	n/a	n/a
36	CEBPB	chr4:129209035-129209668	Hela-S3	cervix:	n/a	n/a
37	MAX	chr4:129208644-129209958	HCT-116	colon:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
38	EGR1	chr4:129208792-129209738	K562	blood:	n/a	chr4:129209045-129209058 chr4:129209153-129209163 chr4:129209154-129209167 chr4:129209137-129209146 chr4:129209479-129209492 chr4:129208975-129208988 chr4:129209107-129209121 chr4:129209111-129209121 chr4:129209110-129209123 chr4:129209044-129209059 chr4:129209109-129209124 chr4:129209152-129209162 chr4:129209110-129209123 chr4:129209373-129209382 chr4:129209136-129209145 chr4:129209045-129209058
39	TAF1	chr4:129208503-129209892	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr4:129208318-129210364	Raji	blood:	n/a	n/a
41	MYC	chr4:129208768-129210294	K562	blood:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
42	USF1	chr4:129208701-129209746	ECC-1	luminal epithelium:	n/a	chr4:129209481-129209497 chr4:129209475-129209491
43	NFYB	chr4:129208745-129209565	K562	blood:	n/a	chr4:129209071-129209086 chr4:129209025-129209040
44	ATF3	chr4:129209189-129209605	A549	lung:	n/a	n/a
45	POLR2A	chr4:129208554-129210025	GM12878	blood:	n/a	n/a
46	EBF1	chr4:129209139-129210063	GM12878	blood:	n/a	n/a
47	POLR2A	chr4:129208736-129209786	GM12878	blood:	n/a	n/a
48	RUNX3	chr4:129209003-129209978	GM12878	blood:	n/a	n/a
49	NR2F2	chr4:129208978-129210099	K562	blood:	n/a	n/a
50	TEAD4	chr4:129209267-129209650	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:85898664..85899226-chr4:129209096..129209733,2	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	chr4:129208995..129209861-chr6:26123953..26124669,2	Hela-S3	cervix:
8	chr4:129191253..129196346-chr4:129207111..129210585,6	MCF-7	breast:
9	chr4:129208294..129210116-chr4:129731375..129734707,3	MCF-7	breast:
10	chr10:65280831..65281707-chr4:129208804..129209479,2	NB4	blood:
11	chr12:132674042..132674756-chr4:129208582..129209342,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000251432	TF binding region
PGRMC2	TF binding region
ENSG00000165476	Chromatin interaction
ENSG00000273077	Chromatin interaction
ENSG00000138709	Chromatin interaction
ENSG00000077684	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000165678	Chromatin interaction
ENSG00000256576	Chromatin interaction
ENSG00000164040	Chromatin interaction
ENSG00000180596	Chromatin interaction

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

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

rs_ID	r²[population]
rs28726176	1.00[AFR][1000 genomes]
rs41297941	1.00[AFR][1000 genomes];1.00[AMR][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: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	chr4:129206000-129209800	Active TSS	HSMMtube	muscle
12	chr4:129206000-129210000	Active TSS	Fetal Stomach	stomach
13	chr4:129206000-129210000	Active TSS	NHLF	lung
14	chr4:129206000-129210200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr4:129206000-129210200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:129206000-129210400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:129206000-129210400	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr4:129206000-129210400	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr4:129206000-129210400	Active TSS	Fetal Intestine Large	intestine
20	chr4:129206000-129210400	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr4:129206000-129210600	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr4:129206000-129210600	Active TSS	A549	lung
23	chr4:129206200-129209800	Active TSS	Rectal Smooth Muscle	rectum
24	chr4:129206200-129209800	Active TSS	Hela-S3	cervix
25	chr4:129206200-129209800	Active TSS	HSMM	muscle
26	chr4:129206200-129210200	Active TSS	Colonic Mucosa	Colon
27	chr4:129206200-129210400	Active TSS	Right Ventricle	heart
28	chr4:129206400-129209800	Active TSS	H1 Cell Line	embryonic stem cell
29	chr4:129206400-129210000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:129206400-129210000	Active TSS	NHDF-Ad	bronchial
31	chr4:129206400-129210200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:129206400-129210400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:129206600-129209600	Active TSS	Placenta	Placenta
34	chr4:129206600-129210000	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr4:129206600-129210200	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr4:129206800-129209600	Active TSS	HMEC	breast
37	chr4:129206800-129209800	Active TSS	Muscle Satellite Cultured Cells	--
38	chr4:129206800-129210000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:129206800-129210000	Active TSS	Brain Germinal Matrix	brain
40	chr4:129206800-129210200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr4:129206800-129210200	Active TSS	Ovary	ovary
42	chr4:129206800-129210400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:129206800-129211000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:129207000-129209800	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr4:129207000-129209800	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr4:129207000-129210000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:129207000-129210400	Active TSS	Placenta Amnion	Placenta Amnion
48	chr4:129207000-129210800	Active TSS	GM12878-XiMat	blood
49	chr4:129207200-129209600	Active TSS	Fetal Muscle Trunk	muscle
50	chr4:129207200-129209800	Active TSS	NHEK	skin

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