Variant report

Variant	rs4925621
Chromosome Location	chr1:247494162-247494163
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	MAX	chr1:247493981-247494174	HepG2	liver:	n/a	n/a
2	SIN3A	chr1:247493833-247497073	H1-hESC	embryonic stem cell:	n/a	chr1:247495631-247495642 chr1:247495953-247495964
3	MAX	chr1:247493795-247494875	ECC-1	luminal epithelium:	n/a	n/a
4	ELF1	chr1:247494100-247496415	GM12878	blood:	n/a	chr1:247495199-247495212 chr1:247494665-247494677 chr1:247496347-247496358
5	POLR2A	chr1:247493944-247495972	H1-neurons	neurons:	n/a	n/a
6	MAX	chr1:247493811-247496029	ECC-1	luminal epithelium:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247494975-247494985 chr1:247495807-247495816
7	NR2F2	chr1:247493875-247495496	K562	blood:	n/a	n/a
8	FOXP2	chr1:247494145-247494932	PFSK-1	brain:	n/a	n/a
9	TBL1XR1	chr1:247493955-247494176	K562	blood:	n/a	n/a
10	POLR2A	chr1:247494011-247495980	GM18951	blood:	n/a	n/a
11	POLR2A	chr1:247493999-247497967	PFSK-1	brain:	n/a	n/a
12	MAX	chr1:247493985-247496466	K562	blood:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247494975-247494985 chr1:247495807-247495816
13	HA-E2F1	chr1:247494053-247496079	MCF-7	breast:	n/a	chr1:247494407-247494416 chr1:247495255-247495264 chr1:247494976-247494985 chr1:247495252-247495264 chr1:247495607-247495616
14	E2F6	chr1:247493931-247496047	K562	blood:	n/a	chr1:247494407-247494416 chr1:247495255-247495264 chr1:247494976-247494985 chr1:247495252-247495264 chr1:247495607-247495616
15	SIN3AK20	chr1:247493952-247495033	MCF-7	breast:	n/a	n/a
16	JUN	chr1:247493352-247496206	K562	blood:	n/a	chr1:247495603-247495612 chr1:247494409-247494418 chr1:247495601-247495610 chr1:247494408-247494417 chr1:247495781-247495789 chr1:247495256-247495265 chr1:247495782-247495793 chr1:247495604-247495613
17	CREB1	chr1:247494145-247495875	HepG2	liver:	n/a	n/a
18	MAX	chr1:247493794-247496726	K562	blood:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247494975-247494985 chr1:247495807-247495816
19	MAZ	chr1:247494071-247495890	GM12878	blood:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247494975-247494985 chr1:247495807-247495816
20	ZEB1	chr1:247494142-247494676	GM12878	blood:	n/a	chr1:247494377-247494386
21	TAF1	chr1:247494126-247495875	ECC-1	luminal epithelium:	n/a	n/a
22	EP300	chr1:247494106-247495956	ECC-1	luminal epithelium:	n/a	chr1:247495201-247495210 chr1:247494427-247494443
23	GTF2F1	chr1:247494088-247494180	K562	blood:	n/a	n/a
24	MYC	chr1:247493850-247496299	K562	blood:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247494975-247494985 chr1:247495807-247495816
25	SMC3	chr1:247494105-247494824	Hela-S3	cervix:	n/a	chr1:247494490-247494500
26	SMARCB1	chr1:247493622-247496851	Hela-S3	cervix:	n/a	n/a
27	MAZ	chr1:247493798-247496834	IMR90	lung:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247494975-247494985 chr1:247495807-247495816
28	E2F1	chr1:247494126-247495922	Hela-S3	cervix:	n/a	chr1:247494407-247494416 chr1:247495255-247495264 chr1:247494976-247494985 chr1:247495252-247495264 chr1:247495607-247495616
29	MXI1	chr1:247493895-247494665	K562	blood:	n/a	n/a
30	TCF12	chr1:247494120-247495529	ECC-1	luminal epithelium:	n/a	chr1:247494982-247494989
31	CHD1	chr1:247493780-247497114	IMR90	lung:	n/a	n/a
32	REST	chr1:247493743-247496638	H1-neurons	neurons:	n/a	chr1:247494276-247494283 chr1:247493797-247493810
33	RCOR1	chr1:247494160-247495230	Hela-S3	cervix:	n/a	n/a
34	E2F6	chr1:247493924-247494174	K562	blood:	n/a	n/a
35	POLR2A	chr1:247493567-247500327	K562	blood:	n/a	n/a
36	POLR2A	chr1:247494014-247496003	H1-neurons	neurons:	n/a	n/a
37	MYC	chr1:247493844-247496528	K562	blood:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247494975-247494985 chr1:247495807-247495816
38	RFX5	chr1:247494120-247494758	Hela-S3	cervix:	n/a	n/a
39	ZNF143	chr1:247494119-247494228	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr1:247493915-247495915	K562	blood:	n/a	n/a
41	MXI1	chr1:247493971-247495900	HepG2	liver:	n/a	n/a
42	POLR2A	chr1:247494104-247497372	H1-hESC	embryonic stem cell:	n/a	n/a
43	PML	chr1:247494018-247496101	GM12878	blood:	n/a	n/a
44	MXI1	chr1:247493467-247496872	IMR90	lung:	n/a	n/a
45	MXI1	chr1:247493694-247497375	SK-N-SH	brain:	n/a	n/a
46	SIN3AK20	chr1:247493871-247496348	K562	blood:	n/a	n/a
47	HMGN3	chr1:247493960-247495864	K562	blood:	n/a	n/a
48	MAX	chr1:247493901-247494908	K562	blood:	n/a	n/a
49	MAX	chr1:247493820-247496138	HCT-116	colon:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247494975-247494985 chr1:247495807-247495816
50	TCF12	chr1:247494090-247496013	ECC-1	luminal epithelium:	n/a	chr1:247494982-247494989 chr1:247495950-247495960

No.	Distal block	Cell Line	Cell type
1	chr1:247237656..247243483-chr1:247491762..247497969,8	K562	blood:
2	chr1:247371907..247375145-chr1:247492885..247497524,4	MCF-7	breast:
3	chr1:247371861..247375582-chr1:247493463..247496360,5	MCF-7	breast:
4	chr1:247493116..247494744-chr1:248019396..248022076,3	K562	blood:
5	chr1:247473800..247482682-chr1:247490121..247498423,19	K562	blood:
6	chr1:247093791..247096097-chr1:247493835..247497465,5	K562	blood:

Variant related genes	Relation type
ZNF496	TF binding region
ENSG00000162714	Chromatin interaction
ENSG00000135747	Chromatin interaction
ENSG00000162722	Chromatin interaction
ENSG00000153207	Chromatin interaction
ENSG00000227671	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10754542	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10754544	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10924983	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10924985	0.84[ASN][1000 genomes]
rs10924989	0.84[ASN][1000 genomes]
rs11578583	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1192830	0.82[ASN][1000 genomes]
rs1192831	0.80[ASN][1000 genomes]
rs1192832	0.81[ASN][1000 genomes]
rs1204493	0.83[ASN][1000 genomes]
rs1616299	0.83[ASN][1000 genomes]
rs1771948	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1778544	0.82[ASN][1000 genomes]
rs1778546	0.81[ASN][1000 genomes]
rs1778549	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2153631	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3850824	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4320815	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4925532	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4925533	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4925534	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4925615	0.83[ASN][1000 genomes]
rs56037169	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56399534	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6674425	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6692645	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7418221	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7528202	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7540329	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7552292	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs875883	0.83[ASN][1000 genomes]
rs9426180	0.83[ASN][1000 genomes]
rs9426181	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9426182	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9426233	0.81[ASN][1000 genomes]
rs9725334	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
3	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a
5	esv1848384	chr1:247485654-247495666	Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
6	nsv873439	chr1:247486736-247549220	Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a
7	esv1811709	chr1:247491143-247495666	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
8	esv1840501	chr1:247491143-247495666	Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4925621	ZNF496	cis	Nerve Tibial	GTEx
rs4925621	ZNF496	cis	Thyroid	GTEx
rs4925621	ZNF496	cis	lung	GTEx
rs4925621	EDIL3	trans	lymphoblastoid	RTeQTL
rs4925621	ZNF496	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247493400-247494200	Enhancers	Primary B cells from cord blood	blood
2	chr1:247493400-247494200	Enhancers	Liver	Liver
3	chr1:247493400-247494200	Flanking Active TSS	Fetal Brain Male	brain
4	chr1:247493400-247494200	Flanking Active TSS	Fetal Brain Female	brain
5	chr1:247493400-247494200	Flanking Active TSS	Fetal Thymus	thymus
6	chr1:247493400-247494200	Flanking Active TSS	GM12878-XiMat	blood
7	chr1:247493400-247494400	Enhancers	Small Intestine	intestine
8	chr1:247493400-247494600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:247493400-247494800	Transcr. at gene 5' and 3'	Dnd41	blood
10	chr1:247493600-247494200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr1:247493600-247494200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:247493600-247494200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr1:247493600-247494200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:247493600-247494200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr1:247493600-247494200	Flanking Active TSS	Brain Angular Gyrus	brain
16	chr1:247493600-247494200	Flanking Active TSS	Brain Anterior Caudate	brain
17	chr1:247493600-247494200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:247493600-247494200	Flanking Active TSS	Fetal Lung	lung
19	chr1:247493600-247494200	Enhancers	Gastric	stomach
20	chr1:247493600-247494200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr1:247493600-247494200	Enhancers	Psoas Muscle	Psoas
22	chr1:247493600-247494200	Flanking Active TSS	Thymus	Thymus
23	chr1:247493600-247494200	Flanking Active TSS	A549	lung
24	chr1:247493600-247494200	Flanking Active TSS	Hela-S3	cervix
25	chr1:247493600-247494200	Flanking Active TSS	HMEC	breast
26	chr1:247493600-247494200	Flanking Active TSS	HSMM	muscle
27	chr1:247493600-247494200	Flanking Active TSS	HUVEC	blood vessel
28	chr1:247493600-247494200	Flanking Active TSS	NHEK	skin
29	chr1:247493600-247494400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr1:247493600-247494400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:247493600-247494400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr1:247493600-247494400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:247493600-247494400	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr1:247493600-247494400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr1:247493600-247494400	Flanking Active TSS	NH-A	brain
36	chr1:247493600-247494600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:247493600-247494600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:247493600-247494600	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr1:247493600-247496400	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr1:247493800-247494200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:247493800-247494200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:247493800-247494200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:247493800-247494200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:247493800-247494200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:247493800-247494200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:247493800-247494200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr1:247493800-247494200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:247493800-247494200	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr1:247493800-247494200	Flanking Active TSS	Brain Germinal Matrix	brain
50	chr1:247493800-247494200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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