Variant report

Variant	rs3795407
Chromosome Location	chr1:184723794-184723795
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	CREB1	chr1:184723623-184724543	HepG2	liver:	n/a	n/a
2	GABPA	chr1:184723208-184724545	MCF-7	breast:	n/a	chr1:184723247-184723256 chr1:184723448-184723457
3	TAF1	chr1:184723686-184724118	H1-neurons	neurons:	n/a	n/a
4	MAX	chr1:184723188-184725080	Hela-S3	cervix:	n/a	chr1:184724820-184724835 chr1:184724822-184724832 chr1:184724820-184724830 chr1:184724823-184724830 chr1:184724818-184724833 chr1:184724821-184724832 chr1:184724822-184724831
5	MXI1	chr1:184722533-184725625	SK-N-SH	brain:	n/a	chr1:184724823-184724832
6	CBX3	chr1:184723113-184725259	K562	blood:	n/a	n/a
7	POLR2A	chr1:184722985-184725090	HepG2	liver:	n/a	n/a
8	SP1	chr1:184723644-184724695	A549	lung:	n/a	n/a
9	SIN3AK20	chr1:184723121-184724089	H1-hESC	embryonic stem cell:	n/a	n/a
10	RELA	chr1:184723254-184724994	GM15510	blood:	n/a	n/a
11	POLR2A	chr1:184723080-184724688	HL-60	blood:	n/a	n/a
12	POLR2A	chr1:184723155-184724579	MCF-7	breast:	n/a	n/a
13	NRF1	chr1:184723616-184724749	GM12878	blood:	n/a	n/a
14	TAF1	chr1:184723624-184724062	PFSK-1	brain:	n/a	n/a
15	NFYB	chr1:184723739-184724870	K562	blood:	n/a	n/a
16	GABPA	chr1:184723785-184724437	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:184722940-184725096	K562	blood:	n/a	n/a
18	TAF1	chr1:184723176-184724647	ECC-1	luminal epithelium:	n/a	n/a
19	RUNX3	chr1:184722691-184725219	GM12878	blood:	n/a	n/a
20	ELF1	chr1:184723152-184724546	GM12878	blood:	n/a	chr1:184724045-184724054 chr1:184724043-184724056 chr1:184724044-184724055 chr1:184724044-184724055
21	SIN3AK20	chr1:184722978-184724133	K562	blood:	n/a	n/a
22	POLR2A	chr1:184723120-184725056	GM12892	blood:	n/a	n/a
23	POLR2A	chr1:184723000-184725204	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr1:184723516-184724840	PFSK-1	brain:	n/a	n/a
25	PML	chr1:184722941-184724743	GM12878	blood:	n/a	n/a
26	EGR1	chr1:184723763-184724133	K562	blood:	n/a	n/a
27	TAF1	chr1:184723722-184724054	GM12892	blood:	n/a	n/a
28	CTCF	chr1:184723760-184723910	GM12867	blood:	n/a	n/a
29	SP2	chr1:184723756-184724410	HepG2	liver:	n/a	n/a
30	POLR2A	chr1:184722816-184724651	GM10847	blood:	n/a	n/a
31	PML	chr1:184723547-184724470	MCF-7	breast:	n/a	n/a
32	GABPA	chr1:184723728-184724573	HL-60	blood:	n/a	n/a
33	POU2F2	chr1:184723735-184724475	GM12891	blood:	n/a	n/a
34	MAX	chr1:184723043-184725073	A549	lung:	n/a	chr1:184724820-184724835 chr1:184724822-184724832 chr1:184724820-184724830 chr1:184724823-184724830 chr1:184724818-184724833 chr1:184724821-184724832 chr1:184724822-184724831
35	ZBTB7A	chr1:184723105-184723922	ECC-1	luminal epithelium:	n/a	n/a
36	THAP1	chr1:184723536-184724324	K562	blood:	n/a	n/a
37	MAX	chr1:184723089-184725060	MCF-7	breast:	n/a	chr1:184724820-184724835 chr1:184724822-184724832 chr1:184724820-184724830 chr1:184724823-184724830 chr1:184724818-184724833 chr1:184724821-184724832 chr1:184724822-184724831
38	RCOR1	chr1:184723689-184725066	K562	blood:	n/a	n/a
39	POLR2A	chr1:184723614-184724556	HUVEC	blood vessel:	n/a	n/a
40	MYC	chr1:184723198-184724402	MCF-7	breast:	n/a	n/a
41	GABPA	chr1:184723723-184724348	HL-60	blood:	n/a	n/a
42	RUNX3	chr1:184723077-184725165	GM12878	blood:	n/a	n/a
43	HEY1	chr1:184723129-184724126	K562	blood:	n/a	n/a
44	TEAD4	chr1:184722594-184725182	K562	blood:	n/a	n/a
45	CREB1	chr1:184723615-184724482	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr1:184723538-184724699	U87	brain:	n/a	n/a
47	MAX	chr1:184723192-184725151	GM12878	blood:	n/a	chr1:184724820-184724835 chr1:184724822-184724832 chr1:184724820-184724830 chr1:184724823-184724830 chr1:184724818-184724833 chr1:184724821-184724832 chr1:184724822-184724831
48	POLR2A	chr1:184723188-184724473	GM12878	blood:	n/a	n/a
49	POLR2A	chr1:184723459-184724605	ECC-1	luminal epithelium:	n/a	n/a
50	TAF1	chr1:184723647-184724625	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:184723118..184724888-chr1:185124173..185126460,2	MCF-7	breast:
2	chr1:28831842..28832710-chr1:184723609..184724521,2	HCT-116	colon:
3	chr1:184721859..184724654-chr1:185126581..185128573,2	MCF-7	breast:
4	chr1:6265897..6266452-chr1:184723541..184724495,2	Hela-S3	cervix:
5	chr1:184722993..184726139-chr1:185013897..185016469,4	K562	blood:

Variant related genes	Relation type
EDEM3	TF binding region
ENSG00000121481	Chromatin interaction
ENSG00000242125	Chromatin interaction
ENSG00000158286	Chromatin interaction
ENSG00000180198	Chromatin interaction
ENSG00000121486	Chromatin interaction
ENSG00000116668	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10797983	1.00[AFR][1000 genomes]
rs10911626	1.00[AFR][1000 genomes]
rs12074980	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2273851	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer 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	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1009529	chr1:184663898-184731215	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv3403637	chr1:184722554-184725102	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184721800-184724600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:184721800-184725200	Active TSS	Psoas Muscle	Psoas
3	chr1:184721800-184725200	Active TSS	Stomach Mucosa	stomach
4	chr1:184722000-184725000	Active TSS	GM12878-XiMat	blood
5	chr1:184722000-184725000	Active TSS	K562	blood
6	chr1:184722200-184724600	Active TSS	Duodenum Mucosa	Duodenum
7	chr1:184722200-184724800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:184722200-184725200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr1:184722200-184725200	Active TSS	Fetal Stomach	stomach
10	chr1:184722200-184725400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:184722400-184724400	Active TSS	Fetal Thymus	thymus
12	chr1:184722400-184724800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:184722400-184725000	Active TSS	Fetal Intestine Large	intestine
14	chr1:184722400-184725000	Active TSS	Thymus	Thymus
15	chr1:184722600-184724000	Active TSS	Right Atrium	heart
16	chr1:184722600-184724400	Active TSS	HepG2	liver
17	chr1:184722600-184724600	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr1:184722600-184724800	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr1:184722600-184724800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr1:184722600-184724800	Active TSS	HSMMtube	muscle
21	chr1:184722600-184725000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:184722600-184725000	Active TSS	Primary T cells fromperipheralblood	blood
23	chr1:184722600-184725000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:184722600-184725000	Active TSS	Brain Hippocampus Middle	brain
25	chr1:184722600-184725000	Active TSS	Fetal Intestine Small	intestine
26	chr1:184722600-184725200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:184722600-184725200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:184722600-184725200	Active TSS	Colonic Mucosa	Colon
29	chr1:184722600-184725200	Active TSS	Right Ventricle	heart
30	chr1:184722600-184725400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:184722800-184724600	Active TSS	Primary monocytes fromperipheralblood	blood
32	chr1:184722800-184724600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:184722800-184724600	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr1:184722800-184724600	Active TSS	Stomach Smooth Muscle	stomach
35	chr1:184722800-184724800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr1:184722800-184724800	Active TSS	Small Intestine	intestine
37	chr1:184722800-184724800	Active TSS	NHDF-Ad	bronchial
38	chr1:184722800-184724800	Active TSS	NHLF	lung
39	chr1:184722800-184725000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:184722800-184725000	Active TSS	Colon Smooth Muscle	Colon
41	chr1:184722800-184725000	Active TSS	Fetal Muscle Trunk	muscle
42	chr1:184722800-184725000	Active TSS	Ovary	ovary
43	chr1:184722800-184725000	Active TSS	Pancreas	Pancrea
44	chr1:184722800-184725200	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr1:184722800-184725200	Active TSS	H1 Cell Line	embryonic stem cell
46	chr1:184722800-184725200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:184722800-184725200	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr1:184723000-184723800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:184723000-184724200	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr1:184723000-184724400	Active TSS	Liver	Liver

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